[fcrepo-user] Fedora 3.3.1 and Muradora

[fe...@fedora-commons.org]

Hi All

 

Has anyone managed to get Fedora 3.3 and Muradora working together?

I am in the process of upgrading from Fedora 3.2.1 to Fedora 3.3.1 to fix the security bug, but am not able to get Muradora's PEP working now.

I was wondering if anyone has a Fedora 3.3 web.xml that's working with Muradora.

 

Here's my stacktrace:

SEVERE: Exception starting filter PEPFilter
javax.servlet.ServletException: Error obtaining ContextHandler
        at melcoe.fedora.pep.rest.PEP.init(PEP.java:191)
        at org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:275)
        at org.apache.catalina.core.ApplicationFilterConfig.setFilterDef(ApplicationFilterConfig.java:397)
        at org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:108)
        at org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:3709)
        at org.apache.catalina.core.StandardContext.start(StandardContext.java:4356)
        at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:791)
        at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:771)
        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:525)
        at org.apache.catalina.startup.HostConfig.deployWAR(HostConfig.java:829)
        at org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:718)
        at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490)
        at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1147)
        at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311)
        at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:117)
        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1053)
        at org.apache.catalina.core.StandardHost.start(StandardHost.java:719)
        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1045)
        at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
        at org.apache.catalina.core.StandardService.start(StandardService.java:516)
        at org.apache.catalina.core.StandardServer.start(StandardServer.java:710)
        at org.apache.catalina.startup.Catalina.start(Catalina.java:578)
        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:288)
        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:413)
Caused by: melcoe.fedora.pep.PEPException: Could not initialise ContextHandler.
        at melcoe.fedora.pep.ContextHandlerImpl.getInstance(ContextHandlerImpl.java:89)
        at melcoe.fedora.pep.rest.PEP.init(PEP.java:188)
        ... 27 more
Caused by: melcoe.fedora.pep.PEPException
        at melcoe.fedora.pep.ContextHandlerImpl.init(ContextHandlerImpl.java:283)
        at melcoe.fedora.pep.ContextHandlerImpl.<init>(ContextHandlerImpl.java:76)
        at melcoe.fedora.pep.ContextHandlerImpl.getInstance(ContextHandlerImpl.java:86)
        ... 28 more
Caused by: java.lang.reflect.InvocationTargetException
        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 melcoe.fedora.pep.ContextHandlerImpl.init(ContextHandlerImpl.java:208)
        ... 30 more
Caused by: java.lang.UnsatisfiedLinkError: no db_java-4.8 in java.library.path
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1682)
        at java.lang.Runtime.loadLibrary0(Runtime.java:823)
        at java.lang.System.loadLibrary(System.java:1030)
        at com.sleepycat.db.internal.db_javaJNI.<clinit>(db_javaJNI.java:52)
        at com.sleepycat.db.internal.DbEnv.<init>(DbEnv.java:264)
        at com.sleepycat.db.EnvironmentConfig.createEnvironment(EnvironmentConfig.java:3910)
        at com.sleepycat.db.EnvironmentConfig.openEnvironment(EnvironmentConfig.java:3863)
        at com.sleepycat.db.Environment.<init>(Environment.java:93)
        at melcoe.xacml.pdp.data.DbXmlPolicyDataManager.<init>(DbXmlPolicyDataManager.java:186)
        at melcoe.xacml.util.PopulatePolicyDatabase.<clinit>(PopulatePolicyDatabase.java:51)
        at melcoe.xacml.pdp.MelcoePDPImpl.<init>(MelcoePDPImpl.java:70)
        at melcoe.fedora.pep.DirectPDPClient.<init>(DirectPDPClient.java:52)

The same instance of dbxml seems to work with Fedora 3.2.1.

 

Any help would be greatly appreciated.

 

Kind regards

 

Martin

[ps552]

hi martin

 

just to confirm it is possible for these to work together – we have a working installation, though not yet live. Our install wouldnt be of much use to you as its deployed on a package installed tomcat and is highly customised to our own needs, much of the default funtionality has been replaced but still – it can be done!

 

 

Cheers
Peri Stracchino
Digital Library Team
University of York
ext 4082

new email address peri.st...@york.ac.uk

[fe...@fedora-commons.org]

Thanks so much for the information, Peri. Much appreciated.

Cheers,

Martin

-----Original Message-----
From: ps552 [mailto:peri.st...@york.ac.uk]
Sent: Monday, 7 February 2011 11:36 PM
To: 'Support and info exchange list for Fedora users.'
Subject: Re: [fcrepo-user] Fedora 3.3.1 and Muradora

hi martin

just to confirm it is possible for these to work together - we have a working installation, though not yet live. Our install wouldnt be of much use to you as its deployed on a package installed tomcat and is highly customised to our own needs, much of the default funtionality has been replaced but still - it can be done!

[fe...@fedora-commons.org]

Hi Doron

Thanks for the info.
I managed to get around this problem by deleting the berkeley jar files from the WEB-INF/lib directory, and then placing the correct ones (for Muradora's XACML - db.jar and dbxml.jar) into the tomcat/lib directory. That way - it will share them, instead of trying to load up multiple copies.

My next problem is that any user that does not have the "public" or "administrator" roles gets a "403 Forbidden" when Muradora tries to access
http://MY_SERVER:8080/fedora/describe?xml=true
So my LDAP users, who are able to login to muradora (using FilterLdap.java), cannot access any records, because of the above 403 error.
It's got me stumped at the moment - and with log4j debug turned on, I get no hints as to what is wrong unfortunately.

The only reason that we're upgrading to Fedora 3.3.1 is to fix the security issue that it addresses.

Kind regards

Martin

-----Original Message-----
From: Shalvi, Doron (NIH/NLM) [C] [mailto:sha...@mail.nlm.nih.gov]
Sent: Tuesday, 8 February 2011 9:05 AM
To: 'fedora-com...@lists.sourceforge.net'
Subject: Re: [fcrepo-user] Fedora 3.3.1 and Muradora

Hi Martin,

We received the same error you did when attempting to deploy Muradora 1.4.0B1 with Fedora 3.3. Fedora 3.3 introduced FESL, which contains the XACML components that came from Muradora. Muradora/FESL loads a native library from the JVM in order to interface with the Berkeley DB; however, this causes a runtime error when the same code tries to load the native library twice - once for Muradora, and once for FESL within Fedora 3.3. The resulting error has to do with a native library already being loaded by another classloader in the same JVM. For this reason, we dropped back down to Fedora 3.2.1 (which does not include FESL), although I suppose you would also be OK running Fedora 3.3+ and Muradora in separate containers.

As we currently don't have a great need for XACML, we have slowly been excising these components from Muradora, with the goal of rewiring it to work with FESL in the latest Fedora, such that they can be deployed on the same container without problems.

Peri - please share your strategy for customizing Muradora and Fedora 3.3+ to work on the same container!

Thanks,

Doron
_________________________
Doron Shalvi
NLM Digital Collections
http://collections.nlm.nih.gov
sha...@mail.nih.gov


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

Message: 3
Date: Mon, 7 Feb 2011 13:35:32 -0000
From: "ps552" <peri.st...@york.ac.uk>

Subject: Re: [fcrepo-user] Fedora 3.3.1 and Muradora
To: "'Support and info exchange list for Fedora users.'"

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