[moby] [MOBY-dev] Registrying a moby service that takes aninput collection

[Arnaud Kerhornou]

Hi Eddie,

I'm the service provider of getUpstreamSeqfromEnsembl and i've checked 
the apache log file, and i get a collection back (giving a list of 
ensembl gene identifiers, 'ENSG00000160087' and 'ENSG00000160182' in a 
text-formatted object):

<moby:mobyData moby:queryID='a1'>
            <moby:Collection moby:articleName='upstream_sequences'>
                
                <moby:Simple><moby:CommentedDNASequence 
namespace='ENSEMBL' id='ENSG00000160087'>
  <Integer namespace="" id="" articleName="Length">2000</Integer>
  <String namespace="" id=""  
articleName="SequenceString">ACCCGTGTAAATAAATCATGTCTCCCTAAAATGTATAAAAGCGAGCTGTGCCACATGCACCTTGGGCACCTCCCGAGATGTCATGGGTGTGTCCTTAACCTTGGCAAAACAAACTTTCTAAAGGGACTGAGACCTTCCTCAGTTTGCACCCTCCAGGCTGGGTTCTCTGTCCCTCAAGCATCCCCTGGCCAGACAATCCCTGCTGTTCAGAGGCAGCCAAGGCTTTCTGGTCCAACCCTGGGGGCTGGAGGAGGTGGGGGCAGGAGGTGGTAACTGGGTTGGGGGATGTTTTCTTGGTTGCCAAAGCAGAGGGTGCCCCCCGCTGCTCAAGATGCTGAGGGTGGTCCCTGTTGTCCTATTCCTGAAGCTGCCAGAGGAAGTCCCTCCGGAGGGCTGGCCCACAGCAGAAGGGCTGCTCCTGCCCTCAGAGGGCAATCTCAGGGTTGAGAAGGTTACAGCCACCATCTGCCACCAACCTAGCTGCTTGTGCCGATCCCACTGGCCAAGGCCATCGGCTCTATGGCTAGAGGCCTGGGCAGCCTGTGTCCTGCTTACCAGAAGGCCACAGATGCGGGTGGGTGGGGTGGTGGGGTCTTGGCAAGACGTGCTGGCCACACCTGTCCGGGGCACCTTCTCCCTGGGGTGTGACTCAGCCATGCTCCTGAGCAGGGGCCTCTGAGTTGAGCCTCGCTGCAGTCTTCCCAGCTGCAGGGCCCCCACAGGTGTGCTGTCATCGCACACTACTGAGGGACAGACAAGGCAGAGCGGGCCTCCATCTGCCGCGGGCCACAGCCGTGAGTGTGCATGCGAGTGGATGTGCTGGTGCCTGTATCTGCGGCCGGTGTGGCTTCCCTCACATAACTTTCCATGCTGTGAAAACAGTTTGGCCTGCCCTGCATGGGAACGGCAGAGGCCTGAGAGGAGGCAGAGGAAGGAGGCTGGATGCTGAGATGTTCTCCGAAGGTGGAGCCGGTGACGGCAGTAATGGAGGCAGGCTGGATTCCCACGGGCTGAGGCTGCGTGGACACTCCTCCTGGCTTCTGCCCCACGGCCTGCAGCAACGTCTCAGACCCACCAAGGTGTCCCAGAGGGCCAGAGTCAGGGCTGAGCATGGACACAGCCTGCCCTCTGCCCGTAGCCACAGCGGGACTGACCCTCAATATTCAGCCACCTTGCTGACCTGTGGTTGTTCCTGAGAGGCAGTCAGGGTTGGGGCAAAGGAGAGGGCCACAGGCAGCCAGGTGGCGAGGTCCACCTCCTGATCCCCCACCAGGGGACCACCCTCAGCTCCCCGCTGTCCTCAGCGGCCTCTCAGGGAGGCGGTGGGCTGCGCGCCTGCCCCCAGCGTCCCACCCCAGCGCCCCGCCACCTACCGCTCTCTCCCAATGTGTCTGGGGTCAGAGAGAGGTGGAGAGGACGCAGCGCCCCGCGCTTTCTGCAGTCTGTCCAAGGGGAGGTCAGGGGCATCCCGGGGCTGGGCAGGCACCTGCAGGGGAGGGTGCTGCGGCGCGGACGTGGGTTGCAAAGAGATGCCACGCGTGTCACTCTCGGGTCCCTGAACGAGAGAGCTCTGAGCTCCCTGGAGCCCAACCCTCCACTGAGCCTCCAGGGGCCCGGGACGCTCCATGCCCGGGCCGCGCCGCGCCTCCCCTAAGGGCCGGGTGGGGCGTGGGAGCGGAGGACAAGGCGGGAGCCGGGAGGCGGGAGGGTCGGGGTTCTTTCTCCACCGGGGTCGCCCTCAGCCGGGCCTGCCGCCCTGGGCCGTGGCACATGGGGAGGGAAGCGCGCGGCTTCGGGGTCTGGGGCTCTCGCGCCCACTAACGGTGCCCGGAGCCGCCCGCCAGTGCGCAAGCGCCGCCCCGCCCCCCGCCCCATCCCCCACCCCGGGGTCGACGGCGACAGAGAGTCGTGGGCGCGGTCCGCCAGTCTGCCTAGAGCGGCCAGCCCTCCCCCTCCCTCCTCACCGCCCCGGACCGCGCACCGGAAGCAGAAGCTAGGCT</String>
  <String namespace="" id=""  
articleName="Description">ENSG00000160087:NCBI35:1:1249158:1251157:-1</String>
</moby:CommentedDNASequence>
</moby:Simple>
            
                <moby:Simple><moby:CommentedDNASequence 
namespace='ENSEMBL' id='ENSG00000160182'>
  <Integer namespace="" id="" articleName="Length">2000</Integer>
  <String namespace="" id=""  
articleName="SequenceString">GGACTTGAGCATTTGTGGATTTTGGCATCCCTGGGTGGGGGGTCCTGAAACCAGTCCCCCAGGGGTACTAAGGGACGACTGCATTGTATTTTAAGTTCATTTTCCCTTTCCCTGGTTAATGAATATTTATTTTGCTTTTCTTTCCCTCCTTTCCTTCCTTCCTTCTTTCCCTGTTTCCAGCTGTTACAAACAATGCTAAAAAGAATATCTTTGCCTGTGTTTTCTTCTGCCCAAGTATGAACATGTTTCTGGGATTAAGAGACCAGGCCTGGAAACAGAAGAATTTGCTGAGCTGTAAAATCTGTATGGCTTAAACCTCACCGAACACTGCCCACCTTTTCTCCAAATGATTGTGCAATTTACATCCCATTTCCAAGAGCCCCCATTTTGATCCGAGAAATTAGAGCAGCGAAAACCACCGTCACTATGAGCACCACCCTGGGCCTGGTGCCCCCGTCCTGTTTTCAATAAACTTAAGCTGACCACAGAGGACACCAGGCCTCGGCCCCTCCCTGGGTCCTGCGGTCAGGCCCCTCCTGGAGACCCTGGCCCAGGAGTGGAGACCCCGGTGCAGGAGTGGCAGCCCTGGAGGAGGGGCTGGGTCCTGGGATGGAGCGAAGAGGAACATGGCCGCCCCCATTCTGGCCCAGGCTCCCCTCCCAGAGGGGCTGCAGAAATGTACTGACTAGGTCACCCAAGAAAAGATAGTACCTTTGTTAGGCTAGCATGCATTTTCCTCAGGGCCTAATTTCTCACTGAAGAAGAAAAGATTTCTCCTGTTGTCCATTTCTTCATGCAGCTCTTCAACAGCTGTTTCTCGAATGCCAATCAAAGCCACTGTTCTAGGGTCTGGGGCCACCTCAAGGCACTAGGAGATGAGGACTTCTGCTCCCATGCGCCCTCCCGTCTGCTGCAGGGAGGAGTGCAATGAATAAATAACCAACATAATGTGTCAGTCACTTGTTTTATCCACCAGGAGGTAATAAGAGCTATGAAAGAGAAAGCTCCGAGCAGGGGAGGGGAGTGAGGCATGGTACAGGAGAGCAGGAGGCTGTCCTCTAAAATACAGGAGTCCAGGGGACCAACTGGGAAGGTGTGGGAGGGGGAGGGAGGGAGCCCCATAGACACAGGGGAGTGAACCACGTTCACTTTGTCAGTTTTTGATGGCAGCTCGTATATACTATTTTTTTCTCCCTCCTGCCCCCAGCCCCTCCCAGAAGGAGACTTAATCTGTCGCTCAGGCTGGAGTGCAGTAGGGTGATCTCGACTCACTGCAACCTCCGCCTCCCAGGTTCAAGTGATTCTCCTGACTTAACCTCCAGAGTAGCTAGGATTACAGGCACCCGCCACCATGCCTGGCTAATTTTTGTATTTTTTTTTTTTGTAGAGACGGGGTTTCGCCATGTTGGCCAGGCTAGTCTCAAACTCCTGACTTTAAGTGATCCGCCTGCTTTGGCCTCCCAAAGTGTTGGGATTACAGGCGTGAGCCACTGCGCCAGGCCTACAATTTCATTATTAAAACAATTCCACTGTAAAAGAATTAGCTTAGGCCTAGACGGAATGGGCTTCATGAGCTCCTTCCCTTCCCCCTGCAAGGTCACGGTGGCCACCCCGTGAGCCACTGTTGTCACGGCCAAGCCTTTTTCCGGCCATCTCTCACTATGAATCACTTCTGCAGTGAGTACAGTATTTACCCTGGCGGGAGGGCCTCTCAGATATGAGTAGGACCTGGATTAAGGTCAGGTTGGAGGAGACTCCCATGGGAAAGAGGGACTTTCTGAATCTCAGATCCCTCAGCCAAGATGACCTCACCACATGTCGTCTCTGTCTATCAGCAAATCCTTCCATGTAGCTTGACCATGTCTAGGAAACACCTTTGATAAAAATCAGTGGAGATTATTGTCTCAGAGGATCCCCGGGCCTCCTTAGGCAAATGTTATCTAACGCTCTTTAAGCAAACAGAGCCTGCCCTATAAAATCCGGGGCTCGGGCGGCCTCTC</String>
  <String namespace="" id=""  
articleName="Description">ENSG00000160182:NCBI35:21:42659714:42661713:-1</String>
</moby:CommentedDNASequence>
</moby:Simple>
            
            </moby:Collection>
        </moby:mobyData>
        </moby:mobyContent></moby:MOBY>

but you're right taverna displays a list of two simple DNASequence 
objects, so i don't understand what i am doing wrong ?

cheers,
Arnaud

Edward Kawas wrote:

>Hi,
>
>The problem is on the side of the service provider:
>
>They advertise a collection as the output, yet this is the
>output:
>
>
><?xml version="1.0" encoding="UTF-8"?>
>    <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>      <moby:mobyContent>
>        <moby:mobyData moby:queryID="a1">
>          <moby:Simple>
>            <moby:CommentedDNASequence namespace="ENSEMBL"
>id="ENSG00000079459">
>              <Integer xmlns="http://www.biomoby.org/moby"
>namespace="" id="" articleName="Length">
>2000
>              </Integer>
>              <String xmlns="http://www.biomoby.org/moby"
>namespace="" id="" articleName="SequenceString">
>TGAATAAAGTTTGCTTCTAAGAGAAGTTACTATTTATTCCTAATTAAATGGGGAGGAAAG
>TCTTTGAAGAGGAACCTCTACTTTACTTTTTATACCGTCATGGCTGGAAACTAAGTTTTT
>AAGATTTTTCTGGGGTTCCCTTGGCCGAGGTGGGGAGTGGGAGGGCTGTCCAGTGGTAGG
>GACTTAGGATTTTTAGTTTACAGTAGTAGGGGAAACACTCTGTAATCTAATACATAAGTA
>AATGATGTATTAGAATATGGTAAATATAGGCAAGTAGACCCCCACTGGGATTAGCAGTGG
>TGGAAATGTGAGAGAGGGCAAACAGGTGGGTCTAGATGAGGTGTGAGCAGACTCGAGGGG
>CACAGGAGTTAGTCAAGCCAGTATCTGGGGGATAGTGCAGGAATAGTGAACAGCTAGACA
>AAAAGTCCTAGGGCCAGAGAAAGCAAAAGCATAAGAGATGGAGGCCAGAGAGGTAATCTG
>GGTGGAAGGCTGCAGCCTCTCAGGATCCCTATAGGTGCTTTGGCTTTTGTTGGAGAGACA
>CTGAACAGCTTTGGGCAGTGAACGTACCTGACAGGTTTCCTGTTTGTTTTTGAGATGAAG
>TCTCGCTCTTGTCCCCCAGGCTGGAGTGCAATAGCGCGATCTCAGCTCACTGCAACCTCT
>GCCTCCTGTGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAGGTAGCTGGGATTATAGGCG
>CCTGCCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGCAGTTTCAGCATGTTG
>GCCAGGCTGGTCTTGAACTCCAGACCTCAGGTGATCCGCCCGCCTTGGCCTCCCAAAGTG
>CTGGGATTACAGGCATGAGCCACCGCGCTCGGCTAGACCTGACAGGTTTTAAAAGGATTA
>CTGGTTGCTGTGTTAAAACAGACTGCAGGATGGCTTAGGTAGCCAGTAGGTTTTTTTTTT
>TTTTTGGAGACGTAGTCTTGCTCTGTTGGCCTGGCTGGAGTGCAGCGGTGTCATCTTGGC
>TCACTGCAAACTCCGCTTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCGGAGTAGT
>TGGGACTACAGGCGCCCACCACCACACTCGGCTTTTTTGTATTTTTAGTAGAGACGGGTT
>TCACCATGTTGGCCAGGATGGTCTCGATCTCTTGACCTCGTGATCCACCCGCCTTGGCCT
>CCCAAAGTGTTGCGATTACAGGCGTGAGCCACCACGCCTGGACGGGTAGCCAGTAGTTTC
>TAGGGCTGGAGAGATCTAGGATGAGAGAAGTTTCCACATTCCTGTTACAGGCTCTCTAAG
>GCTTCAGCTCCTTTTTCTAGGACTAAGCTGGATCTCAAGTAAACACTAGAGAGGGGGCAG
>CTGAAGCTCCAGGAGTGTGTGGGGCTCCCTGGGGCTGGATGGCGGTGGCGGGCAGGCGAG
>CTGGGCTGTGCTCGGGTGTGTTACAGTAAAGACGCCCAGCTTGGCGCTGGCCCGGCCTTT
>TCACGGTTTTAGGCTCTACAGAGAGCGGCTGCAGAGCTCACCCGGCTGGCAGGAGCCACC
>GAGGCCGGACACGTGGGCGACTTATTGACCAAGTGGGGAGGAAGCAGCCCCGCACTGCTC
>TCCCGACTGCGGACCACCGTTGGGCTCCTGCGCATCCTAAGCCCCACCGCCTCACCTCCA
>GTCCCCACAGCGTTCGCGCTCCCAGCCGGGGTAAGCGGAAGAAAACAAAGGCCCGGCTCC
>ATCAGGGCACCAATCCCGCTCGTCGGCCTCTTTCTCGGCCTCCAATGAGCTTCTAGAGTG
>TTATCACGCCAGTCTCCTTCCGCGACTGATTGGCCGGGGTCTTCCTAGTGTGAGCGGCCC
>TGGCCAATCAGCGCCCGTCAGCCCACCCCACGAGGCCGCAGCTAGCCCCGCTGGCGGCCG
>AGGCCGGTTGAAGTGGGCGGAGCGGCGGGCGGGGCGTCGCCGTACTAGGCCTGCCCCCTG
>TCCGGCCAGCCCCTCGAAGC
>              </String>
>              <String xmlns="http://www.biomoby.org/moby"
>namespace="" id="" articleName="Description">
>2222:NCBI35:8:11695664:11697663:1
>              </String>
>            </moby:CommentedDNASequence>
>          </moby:Simple>
>        </moby:mobyData>
>      </moby:mobyContent>
>    </moby:MOBY>
>
>Not a collection.
>
>If you are the service provider, you must ensure that you
>output what you state that you will.
>
>Hope this helps,
>
>Eddie
>
>  
>
>>-----Original Message-----
>>From: moby-dev-bounces at portal.open-bio.org [mailto:moby-
>>dev-bounces at portal.open-bio.org] On Behalf Of Mark
>>Wilkinson
>>Sent: Friday, November 04, 2005 8:06 AM
>>To: Arnaud Kerhornou; Core developer announcements
>>Subject: Re: [moby] [MOBY-dev] Registrying a moby service
>>that takes aninput collection
>>
>>I'll address the first part...
>>
>>
>>
>>    
>>
>>><------------------------------------
>>>
>>>Does it mean the registration has failed ?
>>>      
>>>
>>You need to check the return value of your registration
>>attempt - a
>>small XML object is returned to you that contans (among
>>other things -
>>see the API) a boolean 1/0 as to success or failure of
>>your
>>registration.
>>
>>Your registration was successful (I just checked the
>>database).  The
>>client-side problem is a new one for me.  I'll try to
>>duplicate it here
>>later.
>>
>>The Taverna problem I will leave to Eddie to answer
>>(though I think I
>>know what the answer is)
>>
>>M
>>
>>
>>_______________________________________________
>>MOBY-dev mailing list
>>MOBY-dev at biomoby.org
>>http://www.biomoby.org/mailman/listinfo/moby-dev
>>    
>>
>
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>
>  
>