[fcrepo-user] fedora-rebuild.sh fails when using journaling.

[Javier Molina]

Hi all,

I am in the process to upgrade from Fedora 3.3.1 to 3.6.2

I just noticed that after enabling journaling the fedora-rebuild.sh script won't work anymore.

Basically in fedora.fcfg I added the relevant section for normal mode as described here https://wiki.duraspace.org/display/FEDORA36/Journaling#Journaling-impl-config

When starting the fedora web applications everything looks fine but, when stopping it and running fedora-rebuild.sh  I get a  Error creating bean with name 'org.fcrepo.server.security.Authorization': Bean definition is abstract.

This suggest to me that enabling journaling, introduces more spring beans behind the scenes but I have not been able to figure out where or how, enabling DEBUG logging for springframework in logback.xml shows that it is loading beans from the standard locations in server/conf/spring but it does not reveal much detail about the other locations where it is loadging beans from.

This is a snippet:

************************************************************************

DEBUG (DefaultBeanDefinitionDocumentReader) Loading bean definitions

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.security.AuthorizationConfiguration$created#546ce79d]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.security.AuthorizationConfiguration$created#42dd8bec]

DEBUG (DefaultNamespaceHandlerResolver) Loaded NamespaceHandler mappings: {http://www.springframework.org/schema/task=org.springframework.scheduling.config.TaskNamespaceHandler, http://activemq.apache.org/schema/core=org.apache.xbean.spring.context.v2.XBeanNamespaceHandler, http://www.springframework.org/schema/p=org.springframework.beans.factory.xml.SimplePropertyNamespaceHandler, http://www.w3.org/2006/07/ws-policy=org.apache.cxf.ws.policy.spring.PolicyNamespaceHandler, http://www.springframework.org/schema/lang=org.springframework.scripting.config.LangNamespaceHandler, http://www.springframework.org/schema/util=org.springframework.beans.factory.xml.UtilNamespaceHandler, http://cxf.apache.org/jaxws=org.apache.cxf.jaxws.spring.NamespaceHandler, http://cxf.apache.org/policy=org.apache.cxf.ws.policy.spring.NamespaceHandler, http://www.springframework.org/schema/jee=org.springframework.ejb.config.JeeNamespaceHandler, http://cxf.apache.org/transports/http/configuration=org.apache.cxf.transport.http.spring.NamespaceHandler, http://www.springframework.org/schema/tx=org.springframework.transaction.config.TxNamespaceHandler, http://cxf.apache.org/ws/addressing=org.apache.cxf.ws.addressing.spring.NamespaceHandler, http://cxf.apache.org/simple=org.apache.cxf.frontend.spring.NamespaceHandler, http://www.springframework.org/schema/aop=org.springframework.aop.config.AopNamespaceHandler, http://www.springframework.org/schema/context=org.springframework.context.config.ContextNamespaceHandler, http://cxf.apache.org/core=org.apache.cxf.bus.spring.NamespaceHandler, http://cxf.apache.org/jaxrs=org.apache.cxf.jaxrs.spring.NamespaceHandler, http://www.springframework.org/schema/security=org.springframework.security.config.SecurityNamespaceHandler, http://schemas.xmlsoap.org/ws/2004/09/policy=org.apache.cxf.ws.policy.spring.PolicyNamespaceHandler, http://www.w3.org/ns/ws-policy=org.apache.cxf.ws.policy.spring.PolicyNamespaceHandler, http://cxf.apache.org/bindings/soap=org.apache.cxf.binding.soap.spring.NamespaceHandler}

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#245a690]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#2aba391a]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#27faefe0]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#4b9a6fa1]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#816d9ce]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#14356788]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#3e201c15]

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.config.Parameter#2e13c690]

DEBUG (BeanDefinitionParserDelegate) Using generated bean name [util:list#14512f92] for nested custom element 'util:list'

DEBUG (BeanDefinitionParserDelegate) Neither XML 'id' nor 'name' specified - using generated bean name [org.fcrepo.server.security.impl.SimplePolicyLoader#4a5844db]

INFO (XmlBeanDefinitionReader) Loading XML bean definitions from file [/opt/fedora/fedora-3.6/server/config/spring/doobjectvalidator.xml]

DEBUG (DefaultDocumentLoader) Using JAXP provider [org.apache.xerces.jaxp.DocumentBuilderFactoryImpl]

DEBUG (PluggableSchemaResolver) Found XML schema [http://www.springframework.org/schema/beans/spring-beans-3.0.xsd] in classpath: org/springframework/beans/factory/xml/spring-beans-3.0.xsd

DEBUG (DefaultBeanDefinitionDocumentReader) Loading bean definitions

DEBUG (BeanDefinitionParserDelegate) No XML 'id' specified - using 'org.fcrepo.server.validation.DOObjectValidator' as bean name and [] as aliases

INFO (XmlBeanDefinitionReader) Loading XML bean definitions from file [/opt/fedora/fedora-3.6/server/config/spring/triple-generator.xml]

DEBUG (DefaultDocumentLoader) Using JAXP provider [org.apache.xerces.jaxp.DocumentBuilderFactoryImpl]

DEBUG (PluggableSchemaResolver) Found XML schema [http://www.springframework.org/schema/beans/spring-beans-3.0.xsd] in classpath: org/springframework/beans/factory/xml/spring-beans-3.0.xsd

DEBUG (DefaultBeanDefinitionDocumentReader) Loading bean definitions

INFO (GenericApplicationContext) Refreshing org.springframework.context.support.GenericApplicationContext@3e0d6c32: startup date [Thu Jul 18 11:20:35 EST 2013]; parent: org.springframework.context.support.GenericApplicationContext@42e50215

DEBUG (GenericApplicationContext) Bean factory for org.springframework.context.support.GenericApplicationContext@3e0d6c32: org.springframework.beans.factory.support.DefaultListableBeanFactory@50e68513: defining beans [org.springframework.context.annotation.CommonAnnotationBeanPostProcessor,org.fcrepo.server.security.ContextRegistry,org.fcrepo.server.security.Authorization,org.fcrepo.server.security.AuthorizationConfiguration,policyFinderModules,org.fcrepo.server.security.ContextAttributeFinderModule,org.fcrepo.server.security.ResourceAttributeFinderModule,attributeFinderModules,resourceFinderModules,PDPConfigurationFactory,LegacyPDPConfig,org.fcrepo.server.security.PolicyEnforcementPoint,org.fcrepo.server.validation.DOObjectValidator,org.trippi.io.TripleIteratorFactory,Object-3.0,ContentModel-3.0,ServiceDefinition-3.0,ServiceDeployment-3.0,org.fcrepo.server.resourceIndex.TripleGenerator,org.fcrepo.server.resourceIndex.ModelBasedTripleGenerator,localMySQLPool,localDerbyPool,localOraclePool,localPostgreSQLPool,localMulgaraTriplestore,localPostgresMPTTriplestore,apimUpdateMessages,apimAccessMessages,org.fcrepo.server.storage.lowlevel.ILowlevelStorage,org.fcrepo.server.storage.lowlevel.ILowlevelStorageConfiguration,org.fcrepo.server.security.BackendSecurity,org.fcrepo.server.security.BackendSecurityConfiguration,org.fcrepo.server.storage.DOManager,org.fcrepo.server.storage.DOManagerConfiguration,org.fcrepo.server.management.Management,org.fcrepo.server.management.ManagementConfiguration,org.fcrepo.server.management.ManagementDelegate,org.fcrepo.server.management.ManagementDelegateConfiguration,org.fcrepo.server.access.Access,org.fcrepo.server.access.AccessConfiguration,org.fcrepo.server.access.DynamicAccess,org.fcrepo.server.access.DynamicAccessConfiguration,org.fcrepo.server.search.FieldSearch,org.fcrepo.server.search.FieldSearchConfiguration,org.fcrepo.server.resourceIndex.ResourceIndex,org.fcrepo.server.resourceIndex.ResourceIndexConfiguration,org.fcrepo.oai.OAIProvider,org.fcrepo.oai.OAIProviderConfiguration,org.fcrepo.server.storage.translation.DOTranslator,org.fcrepo.server.storage.translation.DOTranslatorConfiguration,org.fcrepo.server.management.PIDGenerator,org.fcrepo.server.management.PIDGeneratorConfiguration,org.fcrepo.server.messaging.Messaging,org.fcrepo.server.messaging.MessagingConfiguration,org.fcrepo.server.storage.ConnectionPoolManager,org.fcrepo.server.storage.ConnectionPoolManagerConfiguration,org.fcrepo.server.validation.DOValidator,org.fcrepo.server.validation.DOValidatorConfiguration,org.fcrepo.server.storage.ExternalContentManager,org.fcrepo.server.storage.ExternalContentManagerConfiguration,org.trippi.TriplestoreConnector,org.fcrepo.server.resourceIndex.ResourceIndexRebuilder,org.fcrepo.server.utilities.rebuild.SQLRebuilder]; parent: org.springframework.beans.factory.support.DefaultListableBeanFactory@7795c14c

DEBUG (DefaultListableBeanFactory) Creating shared instance of singleton bean 'org.springframework.context.annotation.CommonAnnotationBeanPostProcessor'

****************************************************

And here below is the  output when running fedora-rebuild.sh with the default logback.xml config.

Has anyone come across this? Any suggestion to fix it?

Thanks,

Javier

************************************************************

javier@genesis-cl:/opt/fedora/fedora-3.6/server/bin$ ./fedora-rebuild.sh 

                       Fedora Rebuild Utility

                     ..........................

WARNING: Live rebuilds are not currently supported.

         Make sure your server is stopped before continuing.

Server directory is /opt/fedora/fedora-3.6/server

---------------------------------------------------------------------

ERROR (Server) Fatal error while starting server

org.springframework.beans.factory.BeanIsAbstractException: Error creating bean with name 'org.fcrepo.server.security.Authorization': Bean definition is abstract

        at org.springframework.beans.factory.support.AbstractBeanFactory.checkMergedBeanDefinition(AbstractBeanFactory.java:1208) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:277) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:196) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1079) ~[spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.fcrepo.server.Server.getBean(Server.java:1684) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.management.ManagementModule.postInitModule(ManagementModule.java:180) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.Server.init(Server.java:655) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.RebuildServer.getRebuildInstance(RebuildServer.java:164) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.Rebuild.getServer(Rebuild.java:206) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.Rebuild.getRebuilder(Rebuild.java:268) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.Rebuild.main(Rebuild.java:450) ~[fcrepo-server-3.6.2.jar:na]

Error: Fatal error while starting server

java.lang.RuntimeException: Fatal error while starting server

        at org.fcrepo.server.Server.init(Server.java:695)

        at org.fcrepo.server.utilities.rebuild.RebuildServer.getRebuildInstance(RebuildServer.java:164)

        at org.fcrepo.server.utilities.rebuild.Rebuild.getServer(Rebuild.java:206)

        at org.fcrepo.server.utilities.rebuild.Rebuild.getRebuilder(Rebuild.java:268)

        at org.fcrepo.server.utilities.rebuild.Rebuild.main(Rebuild.java:450)

Caused by: org.springframework.beans.factory.BeanIsAbstractException: Error creating bean with name 'org.fcrepo.server.security.Authorization': Bean definition is abstract

        at org.springframework.beans.factory.support.AbstractBeanFactory.checkMergedBeanDefinition(AbstractBeanFactory.java:1208)

        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:277)

        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:196)

        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1079)

        at org.fcrepo.server.Server.getBean(Server.java:1684)

        at org.fcrepo.server.management.ManagementModule.postInitModule(ManagementModule.java:180)

        at org.fcrepo.server.Server.init(Server.java:655)

        ... 4 more

ERROR (Server) Fatal error while starting server

org.springframework.beans.factory.BeanIsAbstractException: Error creating bean with name 'org.fcrepo.server.security.Authorization': Bean definition is abstract

        at org.springframework.beans.factory.support.AbstractBeanFactory.checkMergedBeanDefinition(AbstractBeanFactory.java:1208) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:277) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:196) ~[spring-beans-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1079) ~[spring-context-3.0.7.RELEASE.jar:3.0.7.RELEASE]

        at org.fcrepo.server.Server.getBean(Server.java:1684) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.management.ManagementModule.postInitModule(ManagementModule.java:180) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.Server.init(Server.java:655) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.RebuildServer.getRebuildInstance(RebuildServer.java:164) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.Rebuild.getServer(Rebuild.java:206) ~[fcrepo-server-3.6.2.jar:na]

        at org.fcrepo.server.utilities.rebuild.Rebuild.main(Rebuild.java:463) ~[fcrepo-server-3.6.2.jar:na]

Server shutdown error: java.lang.RuntimeException: Fatal error while starting server

********************************************************************************

[Benjamin Armintor]

Javier:

  Thanks for this report, too! I've stubbed out an issue to track this problem at https://jira.duraspace.org/browse/FCREPO-1194. We will try to confirm this one as well, and fix for 3.7 if necessary.

- Ben

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[Benjamin Armintor]

Javier:

  Could you please attach your .fcfg file for the server in error?

Thanks,

  Ben

[Benjamin Armintor]

Copying from my JIRA comments:

"I don't think there are any messages broadcast on the indexing of a rebuild- you have to independently rebuild the instances. Given that, the easiest workaround for this problem is to comment out the ManagementDelegate configuration when running the Rebuilder. For 3.7, it should be easy to have the RebuildServer ignore the ManagementDelegate module (mark it as abstract, as it does the Management module)."

Regards,

  Ben

[Javier Molina]

I don't know whether this config is still useful but in any case here you are.

[Javier Molina]

That was my attempt to change from legacy fs to akubra but then from your comment it seems it was also a doomed path.

Anyway akubra will have to wait.

Thanks,

Javier