Re: [fcrepo-user] RI error

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Nigel Thomas

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Jan 8, 2013, 11:25:07 AM1/8/13
to fedora-com...@lists.sourceforge.net
Hello Benjamin / Roland,

I am having similar issues installing Fedora 3.6.2 on vagrant (Ubuntu
12.04 server), with RI index enabled, xacml disabled and
fesl.authz.enabled=true.
I have created a simple puppet module for Fedora 3.6.2 installation at
https://github.com/nigel-v-thomas/puppet-fcrepo, which should help
reproduce the problem.

I have tried installing as root into /usr/share/fedora and
/var/tmp/fedora, with full permission granted to relevant folders. Note
that neither folders are mounts.

If I disable RI index, the install runs fine and data directory is
populated with relevant demo objects, activemq-data, datastreamStore.
This implies permissions can be ruled out.

I have found a previous reference to the problem at
https://jira.duraspace.org/browse/FCREPO-998, however this issue was
resolved in Mulgara 2.1.12, which is packaged with 3.6.2.

Benjamin suggested there may be other reasons?

Any ideas?

Nigel Thomas


Roland van Laar <roland@...> writes:

>
> Hello,
>
>
> On Nov 16, 2012, at 4:43 PM, Benjamin Armintor wrote:
> As you can see at the bottom of the stacktrace, the RI doesn't think
it can write to its index. There are a couple of different ways this
can happen, but the most common is that the user Tomcat is running under
doesn't have write permissions to the RI data directory.
>
>
>
>
> Your assumption is correct. Thank you.
> For future reference: I was running fedora in vagrant with /vagrant
shared with vboxsf on OSX when I switched vboxsf to nfs the problems
were solved.
>
> Regards,
>
> Roland van Laar
>
>
> On Fri, Nov 16, 2012 at 10:17 AM, Roland van Laar
<roland-lLQCDUX...@public.gmane.org> wrote:
> Hello,
> I'm having troubles with installing fedora.
> The following error has to do with RI.
> I installed 3.6.1 with the included tomcat and derby.
> Is this a known bug? Or can I do something to fix this.
> Regards,
> Roland van Laar
> Java:
> java version "1.6.0_37"
> Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)
> The error message:
> ==> ../../tomcat/logs/localhost.2012-11-16.log <==
> Nov 16, 2012 3:13:39 PM org.apache.catalina.core.StandardContext
listenerStart
> SEVERE: Exception sending context initialized event to listener
instance of class org.springframework.web.context.ContextLoaderListener
> org.springframework.beans.factory.BeanCreationException: Error
creating bean with name 'org.fcrepo.server.Server' defined in
ServletContext resource [/WEB-INF/applicationContext.xml]: Invocation of
init method failed; nested exception is java.lang.RuntimeException:
Fatal error while starting server
>
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1422)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:518)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455)
> at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
> at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
> at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
> at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192)
> at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
> at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
> at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
> at
org.springframework.web.context.ContextLoader.createWebApplicationContext(ContextLoader.java:282)
> at
org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:204)
> at
org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:47)
> at
org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4206)
> at
org.apache.catalina.core.StandardContext.start(StandardContext.java:4705)
> at
org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799)
> at
org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779)
> at
org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601)
> at
org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675)
> at
org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601)
> at
org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502)
> at
org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317)
> at
org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324)
> at
org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142)
> at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065)
> at
org.apache.catalina.core.StandardHost.start(StandardHost.java:840)
> at
org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057)
> at
org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463)
> at
org.apache.catalina.core.StandardService.start(StandardService.java:525)
> at
org.apache.catalina.core.StandardServer.start(StandardServer.java:754)
> at org.apache.catalina.startup.Catalina.start(Catalina.java:595)
> 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.apache.catalina.startup.Bootstrap.start(Bootstrap.java:289)
> at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:414)
> Caused by: java.lang.RuntimeException: Fatal error while starting server
> at org.fcrepo.server.Server.init(Server.java:695)
> 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:1546)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1487)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1419)
> ... 36 more
> Caused by: org.springframework.beans.factory.BeanCreationException:
Error creating bean with name
'org.fcrepo.server.resourceIndex.ResourceIndex': Invocation of init
method failed; nested exception is
org.fcrepo.server.errors.ModuleInitializationException: Error
initializing RI
>
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1422)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:518)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:455)
> at
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:293)
> at
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
> at
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:290)
> at
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:192)
> at
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:585)
> at
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
> at
org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:425)
> at org.fcrepo.server.Server.init(Server.java:630)
> ... 43 more
> Caused by: org.fcrepo.server.errors.ModuleInitializationException:
Error initializing RI
> at
org.fcrepo.server.resourceIndex.ResourceIndexModule.initModule(ResourceIndexModule.java:128)
> 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:1546)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1487)
> at
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1419)
> ... 53 more
> Caused by: java.lang.UnsupportedOperationException: This
MulgaraConnector is read-only!
> at
org.trippi.impl.mulgara.MulgaraConnector.getWriter(MulgaraConnector.java:107)
> at
org.fcrepo.server.resourceIndex.ResourceIndexImpl.<init>(ResourceIndexImpl.java:74)
> at
org.fcrepo.server.resourceIndex.ResourceIndexModule.initModule(ResourceIndexModule.java:121)
> ... 60 more
>
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Roland van Laar

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Jan 8, 2013, 11:35:35 AM1/8/13
to Support and info exchange list for Fedora users., Nigel Thomas
On 01/08/2013 05:25 PM, Nigel Thomas wrote:
> Hello Benjamin / Roland,
>
> I am having similar issues installing Fedora 3.6.2 on vagrant (Ubuntu
> 12.04 server), with RI index enabled, xacml disabled and
> fesl.authz.enabled=true.
> I have created a simple puppet module for Fedora 3.6.2 installation at
> https://github.com/nigel-v-thomas/puppet-fcrepo, which should help
> reproduce the problem.
>
> I have tried installing as root into /usr/share/fedora and
> /var/tmp/fedora, with full permission granted to relevant folders. Note
> that neither folders are mounts.
I solved it by using an NFS mount instead of the vboxfs one.
Since you are not using a mount, I'm not sure what the problem might be.

regards,

Roland
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Nigel Thomas

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Jan 9, 2013, 5:20:36 AM1/9/13
to Roland van Laar, Support and info exchange list for Fedora users., Nigel Thomas
A quick update, I was able to resolve the problem by configuring an
external instance of Mulgara. However, note that the external mulgara
instance had to run as root otherwise the same RI error is thrown.

Puppet config for fedora and external mulgara is in
https://github.com/nigel-v-thomas/puppet-fcrepo and
https://github.com/nigel-v-thomas/puppet-mulgara, respectively.

Nigel
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