Hi Hakon,
My guess is that it's picking up an older version of the code from
somewhere, most likely an old plug-in. Did you try to port your existing
app to the new platform, or are you using a completely new archetype?
(and yes, that's a bug in the user manual!)
Tom
Håkon Sagehaug wrote:
> Hi
>
> I tried to run a simple workflow that uses a web service, I made it run
> from the platform a month ago, but when I tried with the new release i
> got this error
>
> Exception in thread "main" java.lang.NoSuchMethodError:
> net.sf.taverna.t2.activities.wsdl.WSDLActivity.addInput(Ljava/lang/String;IZLjava/util/List;Ljava/lang/Class;Lnet/sf/taverna/t2/workflowmodel/Edits;)V
> at
> net.sf.taverna.t2.activities.wsdl.WSDLActivity.configurePorts(WSDLActivity.java:213)
> at
> net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:99)
> at
> net.sf.taverna.t2.activities.wsdl.WSDLActivity.configure(WSDLActivity.java:64)
> at
> net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:76)
> at
> net.sf.taverna.t2.workflowmodel.serialization.xml.ActivityXMLDeserializer.deserializeActivity(ActivityXMLDeserializer.java:105)
> at
> net.sf.taverna.t2.workflowmodel.serialization.xml.ProcessorXMLDeserializer.deserializeProcessor(ProcessorXMLDeserializer.java:62)
> at
> net.sf.taverna.t2.workflowmodel.serialization.xml.DataflowXMLDeserializer.deserializeDataflow(DataflowXMLDeserializer.java:75)
> at
> net.sf.taverna.t2.workflowmodel.serialization.xml.XMLDeserializerImpl.deserializeDataflow(XMLDeserializerImpl.java:74)
> at
> net.sf.taverna.t2.platform.taverna.impl.WorkflowParserImpl.createDataflow(WorkflowParserImpl.java:68)
> at
> no.plab.hakont.taverna.execution.Application.main(Application.java:55)
>
>
> here is my code
>
> ApplicationContext context = new RavenAwareClassPathXmlApplicationContext(
> "context.xml");
> TavernaBaseProfile profile = new TavernaBaseProfile(context);
> System.out.println("Platform created.");
>
> // Do stuff with platform!
> // Your code here...
>
> Enactor enactor = profile.getEnactor();
>
> WorkflowParser parser = profile.getWorkflowParser();
>
> try {
>
> Dataflow data = parser.createDataflow(new
> FileInputStream(new File(
> "/Home/bccs/hakont/TavernaWF/uniprot_pdb.t2flow")));
>
> WorkflowInstanceFacade instance = enactor.createFacade(data);
> ReferenceService ref_service = profile.getReferenceService();
>
> String input = "<unip:GetPDB
> xmlns:unip=\"http://bccs.uib.no/esysbio/service/UniprotParser/\"; "
> +
> "xmlns:unip1=\"http://bccs.uib.no/esysbio//service/UniprotParser\";>"
> +
> "<unip1:Uniprot><unip1:ProteinId>P02931</unip1:ProteinId></unip1:Uniprot></unip:GetPDB>";
>
> List<String> inputs = new LinkedList<String>();
> inputs.add(input);
>
> T2Reference t2_ref = ref_service.register(input, 1, true, null);
>
> enactor.pushData(instance, "Proteinid", t2_ref);
>
> T2Reference outputRef = enactor.waitForResult(instance, "PDB");
>
> any hint on this
>
> Also at page 32 of the manual,
>
> URL workflowURL = new URL("http://foo.com/workflow.xml";)
> Dataflow workflow = parser.createDataflow();
>
> should it not be
>
> URL workflowURL = new URL("http://foo.com/workflow.xml";)
> Dataflow workflow = parser.createDataflow(workflowURL);
>
>
> cheers, Håkon
>
> 2009/2/11 Tom Oinn <[email protected] <mailto:[email protected]>>
>
> Hi all,
>
> I've just done a release of the t2 platform, version p0.1a2. This
> version features numerous bug fixes over the previous alpha, and a much
> more extensive set of plug-ins.
>
> You should be able to run almost any current t2 workflow now, with the
> caveat that beanshells and localworkers which rely on external
> dependencies are not yet implemented.
>
> You'll pick up the new code if you use the updated archetypes, for those
> hardy souls running from CVS you can use the tag 'p01a2'. Artifacts are
> deployed to http://www.cyclonic.org/t2platform/repository/'.
>
> API docs for the core (platform + t2 core APIs) are up at
> http://www.cyclonic.org/t2platform/t2api-p0.1a2/ with those for the core
> extensions at http://www.cyclonic.org/t2platform/t2extensions-p0.1a2/
>
> Finally the current version of the developer's manual is available as a
> PDF from http://www.cyclonic.org/t2platform/t2platform-guide-p0.1a2.pdf
>
> For those of you attending the workshop next week - this is the codebase
> we'll be using for the exercises (subject to any horrific show-stopping
> bugs I find over the next few days of course!). The manual is the same
> as the printed one you'll get at the workshop so no need to print it.
>
> Enjoy!
>
> Tom
>
>
> ------------------------------------------------------------------------------
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> <mailto:[email protected]>
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>
>
>
>
> --
> Håkon Sagehaug, Software Developer
> Parallab, Bergen Center for Computational Science (BCCS)
> UNIFOB AS (University of Bergen Research Company)
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
> software. With Adobe AIR, Ajax developers can use existing skills and code to
> build responsive, highly engaging applications that combine the power of local
> resources and data with the reach of the web. Download the Adobe AIR SDK and
> Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com
>
>
> ------------------------------------------------------------------------
>
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------------------------------------------------------------------------------
Create and Deploy Rich Internet Apps outside the browser with Adobe(R)AIR(TM)
software. With Adobe AIR, Ajax developers can use existing skills and code to
build responsive, highly engaging applications that combine the power of local
resources and data with the reach of the web. Download the Adobe AIR SDK and
Ajax docs to start building applications today-http://p.sf.net/sfu/adobe-com
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