[MOBY-dev] sequence datatypes

[Yogaraj.Khanal at usd.edu]

hi to  all,
i got problem executing this web service can anyone help me

/*
 * Moby.java
 *
 * Created on December 3, 2006, 9:33 AM
 *
 * To change this template, choose Tools | Options and locate the template under
 * the Source Creation and Management node. Right-click the template and choose
 * Open. You can then make changes to the template in the Source Editor.
 */
import org.biomoby.client.*;
import org.biomoby.shared.*;
import org.biomoby.shared.data.*;
/**
 *
 * @author yogaraj.khanal
 */
public class Moby {
    
    /** Creates a new instance of Moby */
    public Moby() {
    }
    
    /**
     * @param args the command line arguments
     */
    public static void main(String[] args) throws Exception{
        Central worker = new CentralImpl();
        MobyService templateService = new MobyService("runGeneIDGFF");
        System.out.println(templateService.getName());
         System.out.println(templateService.getUniqueName());
         System.out.println(templateService.getAuthority());
        MobyPrimaryData[] priinput=templateService.getPrimaryInputs();
        System.out.println(priinput);
        
        MobyService[] validServices = worker.findService(templateService.getId());
        System.out.println(validServices);
        MobyRequest mr = new MobyRequest(worker);
	//mr.setService(validServices[0]);
       
	//mr.setInput(new MobyDataObject("", ""));
	System.out.println(mr.invokeService().toString());

	//MobyRequest mr = new MobyRequest(worker);
	mr.setService(validServices[10]);
        
	mr.setInput(new MobyDataObject("NCBI_gi", "111076"));
        MobyDataType dataType=new MobyDataType("AminoAcidSequence");
        mr.setInput(new MobyDataObject("AminoAcidSequence"));
        MobyDataSecondaryInstance[] secondaryData=new MobyDataSecondaryInstance[5];
        MobySecondaryData p1=new MobySecondaryData("strand");
        p1.setDataType("String");
        p1.setDefaultValue("Reverse");
        MobySecondaryData p2=new MobySecondaryData("profile");
        p2.setDataType("String");
        p2.setDefaultValue("Arabidopsis thalina(weed)");
        MobySecondaryData p3=new MobySecondaryData("engine");
        p3.setDataType("String");
        p3.setDefaultValue("Exon Mode");
        MobySecondaryData p4=new MobySecondaryData("signals");
        p4.setDataType("String");
        p4.setDefaultValue("Start condons");
        MobySecondaryData p5=new MobySecondaryData("exons");
        p5.setDataType("String");
        p5.setDefaultValue("All exons");
        
        secondaryData[0]=new MobyDataSecondaryInstance(p1);
        secondaryData[1]=new MobyDataSecondaryInstance(p2);
        secondaryData[2]=new MobyDataSecondaryInstance(p3);
        secondaryData[3]=new MobyDataSecondaryInstance(p4);
        secondaryData[4]=new MobyDataSecondaryInstance(p5);
        mr.setSecondaryInput(secondaryData);
        
	System.out.println(mr.invokeService().toString());
        // TODO code application logic here
    }
    
}

----- Original Message -----
From: Paul Gordon <gordonp at ucalgary.ca>
Date: Tuesday, December 12, 2006 3:40 pm
Subject: Re: [MOBY-dev] sequence datatypes

> Hi Nassib,
> 
> I looked at the presentation, and I'm not sure why you can't just 
> use a 
> VirtualSequence instead.  You can then have all of the 
> combinations you 
> want, as long as you register the namespaces:
> 
> <VirtualSequence articleName="foo" namespace="renci_global" id="bar">
> <Integer articleName="Length" namespace="" id="">1500</Integer>
> </VirtualSequence>
> 
> <VirtualSequence articleName="foo" namespace="renci_user" id="baz">
> <Integer articleName="Length" namespace="" id="">1500</Integer>
> </VirtualSequence>
> 
> <VirtualSequence articleName="foo" namespace="NCBI_gi" id="123456">
> <Integer articleName="Length" namespace="" id="">1500</Integer>
> </VirtualSequence>
> 
> <DNASequence articleName="foo" namespace="any" id="qux">
> <Integer articleName="Length" namespace="" id="">1500</Integer>
> <String articleName="SequenceString" namespace="" 
> id="">ATG...</String></DNASequence>
> 
> etc., etc.
> > Hi,
> >
> > I'd like to start explaining a little bit about our use of 
> biomoby and
> > also request feedback...
> >
> > We're using biomoby mainly with taverna workflows, and gradually
> > migrating current web services over to become biomoby services 
> (under> biomoby.renci.org).  The workflows we develop are talking 
> to services
> > that for the most part are based here within our servers.  As a 
> result> we end up passing a very large amount of duplicated 
> sequence data over
> > the network between taverna and services, often more data than 
> taverna> is happy about.  To get around this we have started 
> passing sequences
> > by reference using a FASTA-like format that is non-standard but fits
> > well into our system and the taverna UI.  I'm calling this the 
> "RENCI> sequence" format, and it's basically similar to GenBank, while
> > allowing an "abbreviated" (truncated) form that consists of only a
> > partial header line with at least one namespace/id.  (The 
> architecture> is described in 
> http://www.renci.org/~nassar/sequence_registry.ppt )
> >
> > We've added some new datatypes under "RenciSequence" for this 
> purpose,> analogous to the existing "GenericSequence".  In general 
> we are using
> > the existing biomoby datatypes, but for sequences our format seems
> > unusual enough that we thought it needed its own datatype to avoid
> > confusion.
> >
> > Nassib
> > _______________________________________________
> > MOBY-dev mailing list
> > MOBY-dev at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-dev
> >
> >
> >   
> 
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