Hi Peri, We ran into a very similar problem when attempting to rebuild about six weeks ago and (after a lot of very constructive advice from Steve Bayliss) ended up taking the 'nuclear option' of deleting our repository and re-ingesting everything. However it'd be great to know what went wrong.
We actually have an almost identical OS and database set-up to yours so it would be most interesting if you could share your Java environment variables, and any changes that you made to the env-server.sh file. Thanks, Graeme On 22 Nov 2010, at 12:17, ps552 wrote: > thanks chris, scott, steve > > we managed to get the rebuild script working by dropping commons-pool.jar > into /var/lib/tomcat6/common/lib. However I would not be at all surprised if > we were to run into other similar issues so its good to know where to look to > debug. Having said that, the scripts and functions in our version of fedora > (the latest patched version)are differently named - server-env.sh, however I > assume thats just a different naming convention in the later version, since > it seems to be doing pretty much the same tasks > > > ***my email address has changed and may need updating in your address book*** > > Cheers > Peri Stracchino > Digital Library Team > University of York > ext 4082 > new email address peri.stracch...@york.ac.uk > > > -----Original Message----- > From: Chris Wilper [mailto:cwil...@duraspace.org] > Sent: 19 November 2010 17:01 > To: fcrepo-user > Subject: Re: [fcrepo-user] rebuild.sh fails with ModuleInitializationException > > Hi Peri, > > Since you're using the package manager-installed tomcat (and not the > bundled one), you'll probably have to modify the > $FEDORA_HOME/server/bin/env.sh script in order to get the server > scripts to use the correct classpath. When using the bundled tomcat, > we can assume all the .jar files and classes needed are in the places > we expect them to be, but when using a different servlet container, > those assumptions fail. > > See the lines in env.sh that look like this (in the execWithTestArgs > function): > > -cp > \"$webinf\"/classes:\"$FEDORA_HOME\"/server/bin:\"$FEDORA_HOME\"/server/bin/fcrepo-server-3.4.1-cli-loader-main.jar > \ > -Djava.endorsed.dirs=\"$common\"/endorsed:\"$common\"/lib \ > > ...those will have to be adjusted to point to the right directories in > your installation. I recall that the "common/endorsed" and > "common/lib" directories in particular vary in different distributions > of Tomcat, so that's a place to start. > > - Chris > > On Fri, Nov 19, 2010 at 11:19 AM, ps552 <peri.stracch...@york.ac.uk> wrote: >> Hi >> >> We are having a perplexing problem. We have a new installation of >> fedora-commons on a Ubuntu server using package installed tomcat6, and >> MySQL. Weare able to create new objects using the admin client, and also >> ingest objects succesfully using the interface, and afterwards view them >> using fedora/get. However when we try to run the rebuild.sh script it >> manages to clear the existing tables, so is obviously connectling to the >> database,, but then fails with the error below . has anybody else >> expereincedthis behaviour or can throw any light on this for us? >> >> ERROR 2010-11-19 12:09:47.544 [main] (Server) Module >> (org.fcrepo.server.storage.ConnectionPoolManager) failed to initialize >> >> org.fcrepo.server.errors.ModuleInitializationException: A connection pool >> could not be instantiated. The underlying error was a >> java.lang.NoClassDefFoundErrorThe message was >> "org/apache/commons/dbcp/BasicDataSourceFactory". >> >> at >> org.fcrepo.server.storage.ConnectionPoolManagerImpl.initModule(ConnectionPoolManagerImpl.java:270) >> [fcrepo-server-3.4.1.jar:na] >> >> at org.fcrepo.server.Module.<init>(Module.java:64) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.storage.ConnectionPoolManagerImpl.<init>(ConnectionPoolManagerImpl.java:96) >> [fcrepo-server-3.4.1.jar:na] >> >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >> Method) [na:1.6.0_22] >> >> at >> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) >> [na:1.6.0_22] >> >> at >> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) >> [na:1.6.0_22] >> >> at java.lang.reflect.Constructor.newInstance(Constructor.java:513) >> [na:1.6.0_22] >> >> at org.fcrepo.server.Server.<init>(Server.java:567) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.utilities.rebuild.RebuildServer.<init>(RebuildServer.java:43) >> [fcrepo-server-3.4.1.jar:na] >> >> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native >> Method) [na:1.6.0_22] >> >> at >> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39) >> [na:1.6.0_22] >> >> at >> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27) >> [na:1.6.0_22] >> >> at java.lang.reflect.Constructor.newInstance(Constructor.java:513) >> [na:1.6.0_22] >> >> at >> org.fcrepo.server.utilities.rebuild.RebuildServer.getRebuildInstance(RebuildServer.java:120) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.utilities.rebuild.Rebuild.getServer(Rebuild.java:173) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.utilities.rebuild.SQLRebuilder.start(SQLRebuilder.java:112) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.utilities.rebuild.Rebuild.<init>(Rebuild.java:106) >> [fcrepo-server-3.4.1.jar:na] >> >> at >> org.fcrepo.server.utilities.rebuild.Rebuild.main(Rebuild.java:394) >> [fcrepo-server-3.4.1.jar:na] >> >> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) >> [na:1.6.0_22] >> >> at >> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) >> [na:1.6.0_22] >> >> at >> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) >> [na:1.6.0_22] >> >> at java.lang.reflect.Method.invoke(Method.java:597) [na:1.6.0_22] >> >> at >> org.fcrepo.server.utilities.rebuild.cli.CLILoader.main(CLILoader.java:77) >> [fcrepo-server-3.4.1-cli-loader-main.jar:na] >> >> ***my email address has changed and may need updating in your address >> book*** >> >> Cheers >> Peri Stracchino >> Digital Library Team >> University of York >> ext 4082 >> >> new email address peri.stracch...@york.ac.uk >> >> ------------------------------------------------------------------------------ >> Beautiful is writing same markup. 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