On Tue, Mar 3, 2009 at 09:43, Jerzy Orlowski <[email protected]> wrote:
> No, I just make some own libraries for manipulating XML files with
> workflows and I'd like to know what to expect.
> Stian, when can I expect the XSD?
t2flow.xsd in Subversion [1] which I sent a mail about previously
seems to validate various .t2flow's I tested with and should be ready
for you to have a play with.
It does not cover the various configurations, so a separate schema
t2flow-extended.xsd will attempt to roughly describe the current
xstream serialisations for the official dispatch stack layers and
activities. I've just started on this. This is a separate (redefining)
schema as you could use various 3rd-party activity plugins that would
also need to be described separately.
(If you are worried that this takes time away from various other
Taverna issues - I'm doing this on my 15 minutes train rides in the
morning :-) )
> And one more question. I suspect that what I find in activityConfigBean
> in XML represents all the options defined in the activity type.
> Could You describe how are the activity options written into XML and how
> they are parsed from XML?
If the encoding it set to "xstream", they are parsed using xstream [2]
and basically set directly as properties on the configuration bean
classes. To be precise xstream seem to set the private fields without
calling the setWhatever() methods - but that and the actual
serialisation format of the configuration is something we need to
revise later for that reason.
The actual meaning of the configuration is depending on the different
activity implementations.
Normally the configuration attributes have reasonable names, for
instance, here's the configuration for the WSDLActivity:
<activity><raven><group>net.sf.taverna.t2.activities</group><artifact>wsdl-activity</artifact><version>0.4</version></raven><class>net.sf.taverna.t2.activities.wsdl.WSDLActivity</class>
(..)
<configBean encoding="xstream">
<net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean xmlns="">
<wsdl>http://soap.genome.jp/KEGG.wsdl</wsdl>
<operation>get_paralogs_by_gene</operation>
</net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean>
</configBean>
</activity>
When deserialising Taverna would do (in pseudocode) something like:
plugin = raven.getPlugin("net.sf.taverna.t2.activities", "wsdl-activity", "0.4")
activity = plugin.loadClass("net.sf.taverna.t2.activities.wsdl.WSDLActivity")
bean = new net.sf.taverna.t2.activities.wsdl.WSDLActivityConfigurationBean()
bean.wsdl = "http://soap.genome.jp/KEGG.wsdl";
bean.operation = "get_paralogs_by_gene"
activity.configure(bean)
In the revised serialisation format for the t2platform the "raven"
element would pick up the plugin definition as described in the recent
workshop.
[1]
http://code.google.com/p/taverna/source/browse/taverna#taverna/dev/xsd/trunk/t2flow
[2] http://xstream.codehaus.org/
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
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