Re: [Taverna-hackers] Q: Server installation problem, Taverna webapp, ERROR ContextLoader - Context initialization failed, org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'webapp' defined in ServletContext resource

["Hoeftberger, Johann" <Jo...@DFCI.HARVARD.EDU>]

Hello,

I think, I solved my issue, although I understand the situation so far I 
wouldn't expect that behavior at all and it cost me a lot of effort.

On 11/06/2014 11:24 AM, Hoeftberger, Johann wrote:
>>> org.springframework.beans.MethodInvocationException: Property
>>> 'defaultExecuteWorkflowScript' threw exception; nested exception is
>>> java.lang.NullPointerException
>>
>> I'm puzzled as to why it would be setting the
>> defaultExecuteWorkflowScript property and why that would be failing.
>> That's something that is supposed to usually correctly self-bootstrap.
>
> It doesn't in my case. I tried at least seven different installs always
> with the same outcome.
>
>> Do you have anything set for the executeWorkflowScript configuration
>> property? If so, please unset it. The default that is selected (via a
>
> No, not at all!

[...]

>> Principal diagnosis: a null was sent to the method:
>>
>>     void setDefaultExecuteWorkflowScript(String)
>>
>> in the class org.taverna.server.master.localworker.LocalWorkerState
>> which was being instantiated and configured at that point. That
>> particular method is not currently null-safe, but a null ought to not be
>> appearing there either. I've no idea where the null is coming from; it's
>> all driven from a PropertyPlaceholderConfigurer and that doesn't have a
>> null-value set AFAIK.
>>
>> Leaving the property out of your configuration file entirely ought to
>> work. Otherwise, use the string “NONE” (4 chars) explicitly.
>
> I searched in my installation path where I could find the
> "ExecuteWorkflowScript" string and found it in two (relevant) places.
>
> 1. webapps/taverna_server/WEB-INF/beans.xml
> 2. webapps/taverna_server/WEB-INF/classes/WEB-INF/beans.xml
>
> Both files are identical, I didn't change anything about the
> executeWorkflowScript property in these files. The property is set to
> <property name="defaultExecuteWorkflowScript"
> value="${executeWorkflowScript:NONE}" />
>
> I followed your suggestion and commented out the property in both files,
> but that just created an additional error.
> "20141106T110955.486 FATAL Worker SecureFork - no execute workflow script"
> The original error stayed the same. See tavserv.out:

[...]

I found in /webapps/taverna_server/WEB-INF/tavernaserver.properties the 
commented out entry for "executeWorkflowScript:"
I activated this line again and changed its former value of 
"/usr/taverna/executeworkflow.sh"
to 
"WEB-INF/classes/util/taverna-commandline-enterprise-2.5.0/executeworkflow.sh" 
where I found the executeworkflow.sh Bash script.
I changed the file permission of 
WEB-INF/classes/util/taverna-commandline-enterprise-2.5.0/executeworkflow.sh 
to 0754 and restarted the Tomcat server.
Now the Taverna server is running without any error regarding this issue.

(I have one error which says
20141106T134235.797 INFO  forker StdOut - Error: Unable to access 
jarfile [...]/webapps/taverna_server/WEB-INF/classes/util/secure.fork.jar
But that's a different issue I guess.)


> Is there any dependency to a local database (connection) installation?
> Because in the list of logged unresolvable properties I see always some
> database related information. On my system isn't any database system or
> connection installed at all.
> I haven't seen any needed requirements for that in the installation
> procedures.

In the tavserv.out log file I see now logged database activity.

Regards,
Johann

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