Am 01.12.2010 12:16, schrieb Alan R Williams:
> Do you mean when you run it from Eclipse?
>
That's right. And Eclipse runs all modules (jars, classes) in a single 
classpath (I think). But the Taverna logic seperates the classpath for 
every dependency so that you have to deliver the dependencies also in 
every dependency pom file.
This leads me to the idea that the Taverna API itself can't see the 
dependencies and so also not the serialiszation/deserialization classes 
which causes this problem.
A solution would be to avoid using CDK types in the configuration beans.

Am I right?
> It looks as if it can't find org.openscience.cdk.interfaces.IBond which
> appears not to be known to the classloader of
> org.openscience.cdk.applications.taverna.CDKActivityConfigurationBean
That's is right too. Perhaps the problem/solution lies in my explanation 
above.


Cheers,
Andreas

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