soaplab-two-dev

[Soaplab2-dev] making and running services

[Iwe M. <e.c...@gm...>]

Hello Soaplab team,

I have a few issues with soaplab2. Whenever I make small changes to an ACD
file (I am trying to implement a bunch of our group's scripts in soaplab to
make them available for wide use) I have to rebuild the war file, and
restart the tomcat server. I do this with a shell script. The problem is
this takes about a minute. So every change I make takes at least a minute to
test. Is there maybe a better, faster solution?
Soaplab restart script:

sudo ant gensowa
sudo ant jaxdeploy
./tomcat_restart.sh

Another problem I seem to have is an inconsistency in the list of services
after a restart. The spinet application and Taverna recognize the new or
changed services but the list (/services) is not properly refreshed. Taverna
also does not load the new services correctly because it can't find them,
even though they are in the list. The error is shown below:

Caused by:
net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException:
: Unable to call the get spec method for
   endpoint :
http://localhost:8080/soaplab2-axis/services/benchmark_vis.pyramid
   Remote exception message The AXIS engine could not find a target service
to invoke!  targetService is benchmark_vis.pyramid

The last problem is that after conversion of some of the ACD files there
apparently is a problem with the generated XML. Taverna's log file indicates
that with the following error:

Caused by: java.lang.IllegalArgumentException: The char '0x1f' after '' is
not a valid XML character.

I hope this was enough information to help me out a little.

Thanks in advance!

Greetings,

Iwe Muiser

-- 
Iwe EC Muiser
Master student
NTNU - Department of Cancer Research and Molecular Medicine
Bioinformatics & Gene Regulation Group
Laboratory Centre, 5th floor. Erling Skjalgssons gt. 1
Trondheim
+4594157082

Re: [Soaplab2-dev] making and running services

[Mahmut U. <ul...@eb...>]

Hi Iwe,

> I have a few issues with soaplab2. Whenever I make small changes to an
> ACD file (I am trying to implement a bunch of our group's scripts in
> soaplab to make them available for wide use) I have to rebuild the war
> file, and restart the tomcat server. I do this with a shell script.
> The problem is this takes about a minute. So every change I make takes
> at least a minute to test. Is there maybe a better, faster solution? 

Instead of using axis1deploy or jaxdeploy targets you can use
axis1deployx or jaxdeployx targets that should eliminate the need for
restarting the tomcat server (requires Tomcat Web Application Manager).
For testing some of your changes you can use soaplab command line client
using the 'local' protocol which doesn't require re/building soaplab web
application.

> Soaplab restart script:
> 
> sudo ant gensowa
> sudo ant jaxdeploy
> ./tomcat_restart.sh
> 
> Another problem I seem to have is an inconsistency in the list of
> services after a restart. The spinet application and Taverna recognize
> the new or changed services but the list (/services) is not properly
> refreshed. Taverna also does not load the new services correctly
> because it can't find them, even though they are in the list.

This is probably because you are using 'jaxdeploy' rather than
'axis1deploy', taverna soaplab plugin uses axis1 services.

Mahmut