[MOBY-dev] Problems with biomoby plugins in taverna

[Stian Soiland-Reyes]

On Thu, Oct 2, 2008 at 10:31, Jerzy Orlowski <jerzyo at genesilico.pl> wrote:

> What I get is:

> Fetching namespace ontology from
> http://biomoby.org/RESOURCES/MOBY-S/Namespaces
> Exception in thread "Thread-15" java.lang.LinkageError: loader constraint
> violation: loader (instance of
> net/sf/taverna/raven/repository/impl/LocalArtifactClassLoader) previously
> initiated loading for a different type with name
> "org/apache/commons/logging/Log"
>        at org.biomoby.shared.MobyException.<init>(MobyException.java:55)


> - Why do I get such errors?

This might be related to a Raven-related bug with LinkageError we had
earlier, http://www.mygrid.org.uk/dev/issues/browse/TAV-480 although
it then would say "duplicate class definition".



> - Why does the program hang? It should exit with non-zero value

Because the thread running your Biomoby activity fails with a fatal
error, and the workflow never finishes. The program is waiting for the
workflow to finish, but Freefluo doesn't catch LinkageError's which
are RuntimeErrors. (Normally you shouldn't catch RuntimeErrors)


> - Why such workflow does not hang in taverna GUI version (it doesn't prosuce
> any result anyway), I attach the progress report from Taverna GUI version

Probably because classes are initialised in a different order within
the GUI, for instance by the scavengers browsing the service. The
issue happens because of a threading conflict with the classloaders.

> - Why This workflow hangs executeworkflow.sh system? Most of the others work
> ok.

Does it always happen with this workflow..? Which distribution of
Taverna are you using for this?

I am able to reproduce this with Taverna 1.7.1.

I've noted this as a new bug
http://www.mygrid.org.uk/dev/issues/browse/TAV-773 and am quickly
investigating it with a debugger.

It doesn't seem like a concurrency problem, actually, but perhaps
there's twoo different org.apache.commons.logging.Log instances on the
classpath..

this needs further investigation.

-- 
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester