atom feed3 messages in net.sourceforge.lists.taverna-usersRe: [Taverna-users] Java time out exc...
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PaulDec 30, 2010 8:37 am 
Stian Soiland-ReyesJan 4, 2011 1:46 am 
Alexandra NenadicJan 5, 2011 4:37 am 
Subject:Re: [Taverna-users] Java time out exception
From:Alexandra Nenadic (
Date:Jan 5, 2011 4:37:19 am


I will add to FAQ - this is useful to know.

Paul, could you send me an error message please?


On 04/01/2011 09:46, Stian Soiland-Reyes wrote:

On Thu, Dec 30, 2010 at 16:38, Paul<> wrote:

After running a long workflow I have been getting an error, only once out of 300 or so iterations, that says a time out has occurred. This is a Java (Taverna) error, which I fixed in a previous version of Taverna by adding something to the debug.bat file. It has something to do with the amount of time Taverna will wait until it declares a service call as failing. I can't remember what it was though.

(Alex - should we put this in the FAQ? Should include the actual error message.)

I assume we are talking about WSDL services in this case.

A single SOAP or REST call is done as a single HTTP connection, which could easily fail for anything taking more than say 5 minutes. (Our default timeout).

You can tweak Taverna's SOAP timeout by setting a system property -Dtaverna.wsdl.timeout=60 (60 minutes) - but a high value here is only going to be stable on http://localhost or on a locally switched network.

To modify the system property in Windows, modify taverna-debug.bat and start Taverna by double-clicking this file. (These settings won't be picked up by taverna.exe, which is what the Start menu item is launching by default. To modify the start menu item to use taverna-debug.bat instead, right-click on "Taverna workbench 2.2" from the Start menu and go to "Properties")

Edit the end of taverna-debug.bat using Notepad or similar to include the new line:

... set ARGS=%ARGS% -Dsun.swing.enableImprovedDragGesture set ARGS=%ARGS% "-Dtaverna.startup=%TAVERNA_HOME%."

set ARGS=%ARGS% -Dtaverna.wsdl.timeout=60

java %ARGS% -jar "%TAVERNA_HOME%lib\prelauncher-2.2.jar" %* pause

You are also advised for such services in the workflow to use Details->Advanced and set the Retries to say 3 (as the calls would be more likely to fall over due to network trouble) - however if every call is going to take more than 5 minutes you would also need to set the property as above. (otherwise it would just fail after 3x5 minutes)

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