On Wed, Oct 20, 2010 at 00:29, Jane Ren <[email protected]> wrote:
> I need to write some code to make Taverna import our special WSDL services.
> For example, the user enters http://ws.nbcr.net (which contains a bunch of
> applications), and then Taverna loads the individual applications.
This should be possible by providing only a ServiceProvider - which
looks up your applications, and then provides ServiceDescription's
that has WSDLActivity as it's getActivityClass().
How do you get the list of applications from http://ws.nbcr.net - have
you got a program-parseable list of applications there?
You should only need to also implement Activity's if you want to add
specific GUI to support configuration of your service - or you want to
hide or pre/post-process the inputs/outputs of the service. So if you
don't need your own activities, you can change the dependency of
myfancytool-activity-ui to no longer include myfancytool-activity
(which you can delete from the parent project) - and add instead a
dependency on wsdl-activity from Taverna.
You can then also delete the packages that deal with configuration and
display - unless you want to provide a ContextualView that looks up
using your getAppMetadata() methods - I see these provide useful
descriptions about parameters and what the service does. For example
of how a third-party tool can add contextual views - look at the code
for the BioCatalogue plugin [7] - the canHandle() method in the
factory can check if it is an Opal service with the getAppMetadata()
method - and provide the useful information when selecting the service
or one of its input/output ports.
Note that there's a new feature in Taverna 2.2 where you can save a
list of user services from the Taverna workbench - so say you add the
WSDLs and do Right click on 'Available services' and do "Export
services to file" - similarly users can do "Import services from file"
- see attached file with all the services I found on
http://ws.nbcr.net/opal2/dashboard?command=serviceList
> We cannot use the Taverna import WSDL feature for any of our applications
> because our WSDLs are in a different format.
Surely your WSDLs are in the WSDL format..? Are you saying that some
of your WSDL services don't load normally in Taverna if added
manually? If so we would very much like to hear the details about this
as it's likely to be a bug on our side.
> I was able to take the myfancytool example from the Taverna tutorial and
> modify it so that it dynamically generates the ports for one of our
> applications and runs the application.
That sounds like a sensible approach if you decide you do not want to
use the built-in WSDL activity for some of the above reasons. You
would need to dynamically create the ports depending on the service in
question - for the WSDL Activity itself this is done by inspecting the
WSDL and the XML schema - but other activities get this information
from other sources - in some cases the ports are fixed for all
instances of an activity.
If you do this yourself you could try to hide some of the XML
input/output splitters normally required - otherwise - say some
services expect/return nested data structures which would be tricky to
support without the XML splitters, you can depend on the wsdl-activity
[5] and use similar code as in the WSDL activity UI [6] to add
right-click menu items that can add splitters.
>From what I see from your services they are all asynchronous in
nature, so I can see one usecase for building your own activity is to
hide the launchJob()->queryStatus()->getOutputs() cycle - as I guess
launchJobBlocking() might time out for longer-running jobs. This
service architecture is similar to what we've seen for Soaplab - so I
guess you might be interested in looking at the code for Soaplab
activity [1] [2]
It should be possible to build workflows using Taverna and looping
[3], also see an example workflow using a similarly structured EBI
service [4] - you could also share these as a set of workflows in a
myExperiment pack - using the myExperiment plugin users can then add
them as nested workflows - treating them as services.
[1]
http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/tags/activities-1.2/soaplab-activity/
[2]
http://taverna.googlecode.com/svn/taverna/ui/net.sf.taverna.t2.ui-activities/tags/ui-activities-1.2/soaplab-activity-ui/
[3] http://www.mygrid.org.uk/dev/wiki/display/scrap/Looping+in+Taverna+2.1
[4]
http://www.myexperiment.org/workflows/814/download/ebi_interproscan_for_taverna_2_825701.t2flow?version=2
[5]
http://taverna.googlecode.com/svn/taverna/engine/net.sf.taverna.t2.activities/tags/activities-1.2/wsdl-activity/
[6]
http://taverna.googlecode.com/svn/taverna/ui/net.sf.taverna.t2.ui-activities/tags/ui-activities-1.2/wsdl-activity-ui/
[7]
http://mygrid-labs.googlecode.com/svn/biocatalogue-perspective/tags/biocatalogue-perspective-0.1.1/src/main/java/net/sf/taverna/t2/ui/perspectives/biocatalogue/integration/contextual_views/
--
Stian Soiland-Reyes, myGrid team
School of Computer Science
The University of Manchester
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<java.net.URI>
<default>
<string>http://ws.nbcr.net/opal2/services/MAST_4.3.0?wsdl</string>
</default>
</java.net.URI>
</uri>
</net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig>
</configBean>
</provider>
<provider>
<providerId xmlns="http://taverna.sf.net/2008/xml/t2flow";>http://taverna.sf.net/2010/service-provider/wsdl</providerId>
<configBean xmlns="http://taverna.sf.net/2008/xml/t2flow"; encoding="xstream">
<net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig xmlns="">
<uri serialization="custom">
<java.net.URI>
<default>
<string>http://ws.nbcr.net/opal2/services/GLAM2SCAN_4.3.0?wsdl</string>
</default>
</java.net.URI>
</uri>
</net.sf.taverna.t2.activities.wsdl.servicedescriptions.WSDLServiceProviderConfig>
</configBean>
</provider>
</providers>
</serviceDescriptions>------------------------------------------------------------------------------
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