"Please wait while Bamboo sets up your database" has been up for hours postgres

[Gintohewoo]

Ubuntu 18.04 LTS   

OpenJDK 11 

postgres 10

I have tried several times to get Bamboo to setup the database and it invariably just spins with no activity in the system.

I have created a bamboo user on the system, I have created a bamboo user in postgres, created a database, granted all on that database to the bamboo user.

In order to get bamboo setup to launch, i have to cd into

/opt/atlassian/bamboo/atlassian-bamboo-6.7.1/

and execute: sudo bin/start-bamboo.sh

At this point I can load the page at localhost:8085 and start the setup wizard. I put in my license key, give it all the details for the SQL server (I verified I can connect both to/from localhost to postgres and from another server), and when I click "Next," all i get is a page that says "Please wait while Bamboo sets up your database."  This stays up for hours if I let it, there is no activity on the system and nothing written to the database.  I have even tried using the embedded database with the same results.

this is what i see in the catalina.out:

2018-11-13 04:27:18,603 INFO [http-nio-8085-exec-14] [AccessLogFilter] 192.168.1.50 POST http://192.168.1.158:8085/setup/performSetupDatabaseConnection.action 298421kb
2018-11-13 04:27:18,722 INFO [performSetupDatabaseConnectionBackgroundThread] [SetupDatabaseConnectionAction] Validating database configuration...
2018-11-13 04:27:18,731 INFO [performSetupDatabaseConnectionBackgroundThread] [SetupDatabaseConnectionAction] Validating connection to url: [jdbc:postgresql://localhost:5432/bamboo]
2018-11-13 04:27:18,843 INFO [performSetupDatabaseConnectionBackgroundThread] [SetupDatabaseConnectionAction] Database configuration is valid.
2018-11-13 04:27:18,844 INFO [performSetupDatabaseConnectionBackgroundThread] [SetupUtilityBean] Setting up database: postgresql
2018-11-13 04:27:18,844 INFO [performSetupDatabaseConnectionBackgroundThread] [SetupUtilityBean] Bootstrapping database: postgresql
2018-11-13 04:27:18,845 INFO [performSetupDatabaseConnectionBackgroundThread] [DefaultHibernateConfigurator] Saving bootstrap configuration...
2018-11-13 04:27:18,853 INFO [performSetupDatabaseConnectionBackgroundThread] [DefaultHibernateConfigurator] Refreshing Spring context...
2018-11-13 04:27:20,756 WARN [http-nio-8085-exec-14] [TokenHelper] Could not find token mapped to token name: token
2018-11-13 04:27:21,819 WARN [performSetupDatabaseConnectionBackgroundThread] [GenericTypeAwarePropertyDescriptor] Invalid JavaBean property 'mappingResources' being accessed! Ambiguous write methods found next to actually used [public void bucket.core.persistence.hibernate.ConfigurableLocalSessionFactoryBean.setMappingResources(bucket.core.persistence.hibernate.MappingResources)]: [public void org.springframework.orm.hibernate5.LocalSessionFactoryBean.setMappingResources(java.lang.String[])]
2018-11-13 04:27:21,944 WARN [performSetupDatabaseConnectionBackgroundThread] [XmlWebApplicationContext] Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'reloadableBeanFactories' defined in class path resource [applicationContextPlugin.xml]: BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.config.internalTransactionAdvisor': Cannot resolve reference to bean 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0' while setting bean property 'transactionAttributeSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0': BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'customBuildCompleteActionAdvisor' defined in class path resource [applicationContextManagers.xml]: Cannot resolve reference to bean 'hibernateInterceptor' while setting bean property 'advice'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateInterceptor' defined in class path resource [applicationContextPersistence.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [applicationContextPersistence.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
2018-11-13 04:27:21,945 ERROR [performSetupDatabaseConnectionBackgroundThread] [ContextLoader] Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'reloadableBeanFactories' defined in class path resource [applicationContextPlugin.xml]: BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.config.internalTransactionAdvisor': Cannot resolve reference to bean 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0' while setting bean property 'transactionAttributeSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0': BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'customBuildCompleteActionAdvisor' defined in class path resource [applicationContextManagers.xml]: Cannot resolve reference to bean 'hibernateInterceptor' while setting bean property 'advice'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateInterceptor' defined in class path resource [applicationContextPersistence.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [applicationContextPersistence.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:490)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:204)
at org.springframework.context.support.PostProcessorRegistrationDelegate.registerBeanPostProcessors(PostProcessorRegistrationDelegate.java:236)
at org.springframework.context.support.AbstractApplicationContext.registerBeanPostProcessors(AbstractApplicationContext.java:710)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:535)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:409)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:291)
at com.atlassian.config.spring.BootstrappedContainerContext.refresh(BootstrappedContainerContext.java:22)
at com.atlassian.bamboo.setup.DefaultHibernateConfigurator.refreshSpringContextAndCreateDatabase(DefaultHibernateConfigurator.java:120)
at com.atlassian.bamboo.setup.DefaultHibernateConfigurator.configureDatabase(DefaultHibernateConfigurator.java:63)
at com.atlassian.config.bootstrap.DefaultAtlassianBootstrapManager.bootstrapDatabase(DefaultAtlassianBootstrapManager.java:254)
at com.atlassian.bamboo.ww2.actions.setup.SetupUtilityBean.setupStandardDatabase(SetupUtilityBean.java:187)
at com.atlassian.bamboo.ww2.actions.setup.SetupDatabaseConnectionAction.execute(SetupDatabaseConnectionAction.java:87)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at ognl.OgnlRuntime.invokeMethod(OgnlRuntime.java:899)
at ognl.OgnlRuntime.callAppropriateMethod(OgnlRuntime.java:1544)
at ognl.ObjectMethodAccessor.callMethod(ObjectMethodAccessor.java:68)
at com.opensymphony.xwork2.ognl.accessor.XWorkMethodAccessor.callMethodWithDebugInfo(XWorkMethodAccessor.java:98)
at com.opensymphony.xwork2.ognl.accessor.XWorkMethodAccessor.callMethod(XWorkMethodAccessor.java:90)
at ognl.OgnlRuntime.callMethod(OgnlRuntime.java:1620)
at ognl.ASTMethod.getValueBody(ASTMethod.java:91)
at ognl.SimpleNode.evaluateGetValueBody(SimpleNode.java:212)
at ognl.SimpleNode.getValue(SimpleNode.java:258)
at ognl.Ognl.getValue(Ognl.java:470)
at ognl.Ognl.getValue(Ognl.java:434)
at com.opensymphony.xwork2.ognl.OgnlUtil$3.execute(OgnlUtil.java:401)
at com.opensymphony.xwork2.ognl.OgnlUtil.compileAndExecuteMethod(OgnlUtil.java:453)
at com.opensymphony.xwork2.ognl.OgnlUtil.callMethod(OgnlUtil.java:399)
at com.opensymphony.xwork2.DefaultActionInvocation.invokeAction(DefaultActionInvocation.java:438)
at com.opensymphony.xwork2.DefaultActionInvocation.invokeActionOnly(DefaultActionInvocation.java:293)
at org.apache.struts2.interceptor.BackgroundProcess$1.run(BackgroundProcess.java:55)
at java.base/java.lang.Thread.run(Thread.java:834)
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.config.internalTransactionAdvisor': Cannot resolve reference to bean 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0' while setting bean property 'transactionAttributeSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0': BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'customBuildCompleteActionAdvisor' defined in class path resource [applicationContextManagers.xml]: Cannot resolve reference to bean 'hibernateInterceptor' while setting bean property 'advice'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateInterceptor' defined in class path resource [applicationContextPersistence.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [applicationContextPersistence.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:378)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1602)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1354)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:572)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:204)
at org.springframework.aop.framework.autoproxy.BeanFactoryAdvisorRetrievalHelper.findAdvisorBeans(BeanFactoryAdvisorRetrievalHelper.java:91)
at org.springframework.aop.framework.autoproxy.AbstractAdvisorAutoProxyCreator.findCandidateAdvisors(AbstractAdvisorAutoProxyCreator.java:109)
at org.springframework.aop.aspectj.annotation.AnnotationAwareAspectJAutoProxyCreator.findCandidateAdvisors(AnnotationAwareAspectJAutoProxyCreator.java:92)
at org.springframework.aop.aspectj.autoproxy.AspectJAwareAdvisorAutoProxyCreator.shouldSkip(AspectJAwareAdvisorAutoProxyCreator.java:101)
at org.springframework.aop.framework.autoproxy.AbstractAutoProxyCreator.postProcessBeforeInstantiation(AbstractAutoProxyCreator.java:254)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInstantiation(AbstractAutowireCapableBeanFactory.java:1060)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.resolveBeforeInstantiation(AbstractAutowireCapableBeanFactory.java:1033)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:484)
... 37 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'org.springframework.transaction.annotation.AnnotationTransactionAttributeSource#0': BeanPostProcessor before instantiation of bean failed; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'customBuildCompleteActionAdvisor' defined in class path resource [applicationContextManagers.xml]: Cannot resolve reference to bean 'hibernateInterceptor' while setting bean property 'advice'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateInterceptor' defined in class path resource [applicationContextPersistence.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [applicationContextPersistence.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:490)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:367)
... 54 more
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'customBuildCompleteActionAdvisor' defined in class path resource [applicationContextManagers.xml]: Cannot resolve reference to bean 'hibernateInterceptor' while setting bean property 'advice'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hibernateInterceptor' defined in class path resource [applicationContextPersistence.xml]: Cannot resolve reference to bean 'sessionFactory' while setting bean property 'sessionFactory'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'sessionFactory' defined in class path resource [applicationContextPersistence.xml]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:378)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:110)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1602)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1354)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:572)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:495)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:204)
at org.springframework.aop.framework.autoproxy.BeanFactoryAdvisorRetrievalHelper.findAdvisorBeans(BeanFactoryAdvisorRetrievalHelper.java:91)
at org.springframework.aop.framework.autoproxy.AbstractAdvisorAutoProxyCreator.findCandidateAdvisors(AbstractAdvisorAutoProxyCreator.java:109)
at org.springframework.aop.aspectj.annotation.AnnotationAwareAspectJAutoProxyCreator.findCandidateAdvisors(AnnotationAwareAspectJAutoProxyCreator.java:92)
at org.springframework.aop.aspectj.autoproxy.AspectJAwareAdvisorAutoProxyCreator.shouldSkip(AspectJAwareAdvisorAutoProxyCreator.java:101)
at org.springframework.aop.framework.autoproxy.AbstractAutoProxyCreator.postProcessBeforeInstantiation(AbstractAutoProxyCreator.java:254)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInstantiation(AbstractAutowireCapableBeanFactory.java:1060)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.resolveBeforeInstantiation(AbstractAutowireCapableBeanFactory.java:1033)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:484)
... 59 more

I am sure there is more I can provide if needed, I am at a loss and look forward to any advice folks can offer, thank you!

[Michael Wolfe]

@Gintohewoo did you find a solution to this?  Just getting Bamboo installed and I have JDK 1.8 that I downloaded from Oracle's web site and I'm getting this error too. 

[Michael Wolfe]

This fixed my problem:

add-apt-repository ppa:webupd8team/java

apt update

apt install oracle-java8-installer

apt install oracle-java8-set-default

[Gintohewoo]

This is my DB user and creation script run as postgres:

CREATE DATABASE bamboo;
CREATE USER bamboouser WITH ENCRYPTED PASSWORD 'xxxxxxx';
GRANT ALL PRIVILEGES ON DATABASE bamboo TO bamboouser;

followed by:

ALTER DATABASE bamboo OWNER TO bamboouser;

it looks like this:

postgres=# \l
List of databases
Name | Owner | Encoding | Collate | Ctype | Access privileges
------------+----------------+----------+-------------+-------------+-----------------------------------
bamboo | bamboouser | UTF8 | en_US.UTF-8 | en_US.UTF-8 | =Tc/bamboouser +
| | | | | bamboouser=CTc/bamboouser

[Gintohewoo]

I also followed these steps when setting up the connection to Postgres:

https://confluence.atlassian.com/bamboo/postgresql-289276816.html

[Nic Brough -Adaptavist-]

I'm not 100% sure of how OpenJDK numbers itself, but https://confluence.atlassian.com/bamboo/supported-platforms-289276764.html says you need OpenJDK 1.8, not 11  - if those are not equivalent (like we sometimes talk about Oracle Java 1.8 as "8"), then you should try it with a supported JDK instead.

[Gintohewoo]

I tried with both oracle's java 1.8 and openJDK 1.8 with the same results.

OpenJDK's numbering is the same as Oracles as well.