Hello Alan,
thank you for answering!
>> I got the taverna server executing my workflows now.
>>
>
> Is it the downloaded war that you are running?
>
>
Yes, it is the war file version 0.2.1
>> The server may not
>> be restarted in Tomcat, because it will not work after that (it is a
>> known issue, however, the proposed solution deleting sessions.ser and
>> the database lock files is of no help for me). Instead, you have to
>> undeploy the server and deploy it again.
>>
>
> That should have been fixed. When you say "it will not work after
> that", does it start up and then you cannot run workflows properly.
> There was a bug about the order in which the plugins were loaded.
>
>
Well most of the time I cannot run workflows properly. Sometimes the
server won't start. I have those problems on Vista (Tomcat 6.0.20, Java
1.6.0_17) and Ubuntu 9.04 (Tomcat from the Ubuntu repositories, Sun Java
1.6.0_16).
BUT it works fine now in Ubuntu 9.10 (with a manual installation of
Tomcat). I.e., I can start/stop/reload the server in the Tomcat manager
and restart Tomcat itself. So, the problem is solved for me right now.
>> The problem I have now is that a workflow will not execute, if it
>> contains at least one of the "local services" from the taverna workbench
>> (for example encode_byte_to_base64). Has anyboby experience with that?
>> The workflow jobs just stay in status CREATED. It seems like some
>> libraries from the workbench are missing in the server.
>>
>
> How do you create the workflows? Is it with Taverna 2 or 2.1b2? I'll
> see if I can replicate the problem on my machine.
>
>
It is Taverna 2.1b2. A trivial example you can try is the following:
1) String_constant[SomeString] -> out
2) String_constant[SomeString] -> Decode_Base_64_to_byte_Array ->
Encode_Byte_Array_to_Base_64 -> out
The first one works fine both in Taverna workbench and server. The
second one does not work in the server.
The important line in my code seems to be:
Long jobID = tavernaRESTClient.addJob(workflowID, null);
The jobID is in the second example always null. And there is a run-time
exception:
javax.xml.bind.DataBindingException: javax.xml.bind.UnmarshalException
- with linked exception:
[org.xml.sax.SAXParseException: Premature end of file.]
In the Tomcat log files I also find:
net.sf.taverna.t2.workflowmodel.serialization.DeserializationException:
An error occurred deserializing the
dataflow:net.sf.taverna.raven.repository.BasicArtifact :
...
/net.sf.taverna.t2.activities.localworker.LocalworkerActivityConfigurationBean/artifactDependencies/net.sf.taverna.raven.repository.BasicArtifact
...
Caused by: com.thoughtworks.xstream.mapper.CannotResolveClassException:
net.sf.taverna.raven.repository.BasicArtifact :
net.sf.taverna.raven.repository.BasicArtifact
and (strangely)
Class java.lang.Long can not be instantiated using a constructor with a
single String argument
Regards,
Dennis
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