[moby] [MOBY-dev] Registrying a moby service that takes aninputcollection
Edward Kawas
edward.kawas at gmail.com
Fri Nov 4 17:49:33 UTC 2005
Sorry, it turns out you did nothing wrong.
You found a bug that I have fixed and will commit to the
Taverna cvs as soon as I stop getting timeout errors. In the
meantime, download the taverna1.3.jar from the following
location:
http://bioinfo.icapture.ubc.ca/ekawas/jars/
and replace the one in the taverna-workbench-1.3/lib
directory.
Thanks,
Eddie
> -----Original Message-----
> From: moby-dev-bounces at portal.open-bio.org [mailto:moby-
> dev-bounces at portal.open-bio.org] On Behalf Of Arnaud
> Kerhornou
> Sent: Friday, November 04, 2005 9:22 AM
> To: Core developer announcements
> Subject: Re: [moby] [MOBY-dev] Registrying a moby service
> that takes aninputcollection
>
> 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">ACCCGTGTAAATAAATCATGTCTCCCTAA
> AATGTATAAAAGCGAGCTGTGCCACATGCACCTTGGGCACCTCCCGAGATGTCATGGG
> TGTGTCCTTAACCTTGGCAAAACAAACTTTCTAAAGGGACTGAGACCTTCCTCAGTTT
> GCACCCTCCAGGCTGGGTTCTCTGTCCCTCAAGCATCCCCTGGCCAGACAATCCCTGC
> TGTTCAGAGGCAGCCAAGGCTTTCTGGTCCAACCCTGGGGGCTGGAGGAGGTGGGGGC
> AGGAGGTGGTAACTGGGTTGGGGGATGTTTTCTTGGTTGCCAAAGCAGAGGGTGCCCC
> CCGCTGCTCAAGATGCTGAGGGTGGTCCCTGTTGTCCTATTCCTGAAGCTGCCAGAGG
> AAGTCCCTCCGGAGGGCTGGCCCACAGCAGAAGGGCTGCTCCTGCCCTCAGAGGGCAA
> TCTCAGGGTTGAGAAGGTTACAGCCACCATCTGCCACCAACCTAGCTGCTTGTGCCGA
> TCCCACTGGCCAAGGCCATCGGCTCTATGGCTAGAGGCCTGGGCAGCCTGTGTCCTGC
> TTACCAGAAGGCCACAGATGCGGGTGGGTGGGGTGGTGGGGTCTTGGCAAGACGTGCT
> GGCCACACCTGTCCGGGGCACCTTCTCCCTGGGGTGTGACTCAGCCATGCTCCTGAGC
> AGGGGCCTCTGAGTTGAGCCTCGCTGCAGTCTTCCCAGCTGCAGGGCCCCCACAGGTG
> TGCTGTCATCGCACACTACTGAGGGACAGACAAGGCAGAGCGGGCCTCCATCTGCCGC
> GGGCCACAGCCGTGAGTGTGCATGCGAGTGGATGTGCTGGTGCCTGTATCTGCGGCCG
> GTGTGGCTTCCCTCACATAACTTTCCATGCTGTGAAAACAGTTTGGCCTGCCCTGCAT
> GGGAACGGCAGAGGCCTGAGAGGAGGCAGAGGAAGGAGGCTGGATGCTGAGATGTTCT
> CCG!
> AAGGTGGAGCCGGTGACGGCAGTAATGGAGGCAGGCTGGATTCCCACGGGCTGAGGCT
> GCGTGGACACTCCTCCTGGCTTCTGCCCCACGGCCTGCAGCAACGTCTCAGACCCACC
> AAGGTGTCCCAGAGGGCCAGAGTCAGGGCTGAGCATGGACACAGCCTGCCCTCTGCCC
> GTAGCCACAGCGGGACTGACCCTCAATATTCAGCCACCTTGCTGACCTGTGGTTGTTC
> CTGAGAGGCAGTCAGGGTTGGGGCAAAGGAGAGGGCCACAGGCAGCCAGGTGGCGAGG
> TCCACCTCCTGATCCCCCACCAGGGGACCACCCTCAGCTCCCCGCTGTCCTCAGCGGC
> CTCTCAGGGAGGCGGTGGGCTGCGCGCCTGCCCCCAGCGTCCCACCCCAGCGCCCCGC
> CACCTACCGCTCTCTCCCAATGTGTCTGGGGTCAGAGAGAGGTGGAGAGGACGCAGCG
> CCCCGCGCTTTCTGCAGTCTGTCCAAGGGGAGGTCAGGGGCATCCCGGGGCTGGGCAG
> GCACCTGCAGGGGAGGGTGCTGCGGCGCGGACGTGGGTTGCAAAGAGATGCCACGCGT
> GTCACTCTCGGGTCCCTGAACGAGAGAGCTCTGAGCTCCCTGGAGCCCAACCCTCCAC
> TGAGCCTCCAGGGGCCCGGGACGCTCCATGCCCGGGCCGCGCCGCGCCTCCCCTAAGG
> GCCGGGTGGGGCGTGGGAGCGGAGGACAAGGCGGGAGCCGGGAGGCGGGAGGGTCGGG
> GTTCTTTCTCCACCGGGGTCGCCCTCAGCCGGGCCTGCCGCCCTGGGCCGTGGCACAT
> GGGGAGGGAAGCGCGCGGCTTCGGGGTCTGGGGCTCTCGCGCCCACTAACGGTGCCCG
> GAGCCGCCCGCCAGTGCGCAAGCGCCGCCCCGCCCCCCGCCCCATCCCCCACCCCGGG
> GTCGACGGCGACAGAGAGTCGTGGGCGCGGTCCGCCAGTCTGCCTAGAGCGGCCAGCC
> CTC!
> CCCCTCCCTCCTCACCGCCCCGGACCGCGCACCGGAAGCAGAAGCTAGGCT</Strin
> g>
> <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">GGACTTGAGCATTTGTGGATTTTGGCATC
> CCTGGGTGGGGGGTCCTGAAACCAGTCCCCCAGGGGTACTAAGGGACGACTGCATTGT
> ATTTTAAGTTCATTTTCCCTTTCCCTGGTTAATGAATATTTATTTTGCTTTTCTTTCC
> CTCCTTTCCTTCCTTCCTTCTTTCCCTGTTTCCAGCTGTTACAAACAATGCTAAAAAG
> AATATCTTTGCCTGTGTTTTCTTCTGCCCAAGTATGAACATGTTTCTGGGATTAAGAG
> ACCAGGCCTGGAAACAGAAGAATTTGCTGAGCTGTAAAATCTGTATGGCTTAAACCTC
> ACCGAACACTGCCCACCTTTTCTCCAAATGATTGTGCAATTTACATCCCATTTCCAAG
> AGCCCCCATTTTGATCCGAGAAATTAGAGCAGCGAAAACCACCGTCACTATGAGCACC
> ACCCTGGGCCTGGTGCCCCCGTCCTGTTTTCAATAAACTTAAGCTGACCACAGAGGAC
> ACCAGGCCTCGGCCCCTCCCTGGGTCCTGCGGTCAGGCCCCTCCTGGAGACCCTGGCC
> CAGGAGTGGAGACCCCGGTGCAGGAGTGGCAGCCCTGGAGGAGGGGCTGGGTCCTGGG
> ATGGAGCGAAGAGGAACATGGCCGCCCCCATTCTGGCCCAGGCTCCCCTCCCAGAGGG
> GCTGCAGAAATGTACTGACTAGGTCACCCAAGAAAAGATAGTACCTTTGTTAGGCTAG
> CATGCATTTTCCTCAGGGCCTAATTTCTCACTGAAGAAGAAAAGATTTCTCCTGTTGT
> CCATTTCTTCATGCAGCTCTTCAACAGCTGTTTCTCGAATGCCAATCAAAGCCACTGT
> TCTAGGGTCTGGGGCCACCTCAAGGCACTAGGAGATGAGGACTTCTGCTCCCATGCGC
> CCTCCCGTCTGCTGCAGGGAGGAGTGCAATGAATAAATAACCAACATAATGTGTCAGT
> CAC!
> TTGTTTTATCCACCAGGAGGTAATAAGAGCTATGAAAGAGAAAGCTCCGAGCAGGGGA
> GGGGAGTGAGGCATGGTACAGGAGAGCAGGAGGCTGTCCTCTAAAATACAGGAGTCCA
> GGGGACCAACTGGGAAGGTGTGGGAGGGGGAGGGAGGGAGCCCCATAGACACAGGGGA
> GTGAACCACGTTCACTTTGTCAGTTTTTGATGGCAGCTCGTATATACTATTTTTTTCT
> CCCTCCTGCCCCCAGCCCCTCCCAGAAGGAGACTTAATCTGTCGCTCAGGCTGGAGTG
> CAGTAGGGTGATCTCGACTCACTGCAACCTCCGCCTCCCAGGTTCAAGTGATTCTCCT
> GACTTAACCTCCAGAGTAGCTAGGATTACAGGCACCCGCCACCATGCCTGGCTAATTT
> TTGTATTTTTTTTTTTTGTAGAGACGGGGTTTCGCCATGTTGGCCAGGCTAGTCTCAA
> ACTCCTGACTTTAAGTGATCCGCCTGCTTTGGCCTCCCAAAGTGTTGGGATTACAGGC
> GTGAGCCACTGCGCCAGGCCTACAATTTCATTATTAAAACAATTCCACTGTAAAAGAA
> TTAGCTTAGGCCTAGACGGAATGGGCTTCATGAGCTCCTTCCCTTCCCCCTGCAAGGT
> CACGGTGGCCACCCCGTGAGCCACTGTTGTCACGGCCAAGCCTTTTTCCGGCCATCTC
> TCACTATGAATCACTTCTGCAGTGAGTACAGTATTTACCCTGGCGGGAGGGCCTCTCA
> GATATGAGTAGGACCTGGATTAAGGTCAGGTTGGAGGAGACTCCCATGGGAAAGAGGG
> ACTTTCTGAATCTCAGATCCCTCAGCCAAGATGACCTCACCACATGTCGTCTCTGTCT
> ATCAGCAAATCCTTCCATGTAGCTTGACCATGTCTAGGAAACACCTTTGATAAAAATC
> AGTGGAGATTATTGTCTCAGAGGATCCCCGGGCCTCCTTAGGCAAATGTTATCTAACG
> CTC!
> TTTAAGCAAACAGAGCCTGCCCTATAAAATCCGGGGCTCGGGCGGCCTCTC</Strin
> g>
> <String namespace="" id=""
> articleName="Description">ENSG00000160182:NCBI35:21:426597
> 14:42661713:-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">
> >TGAATAAAGTTTGCTTCTAAGAGAAGTTACTATTTATTCCTAATTAAATGGGGAGGA
> AAG
> >TCTTTGAAGAGGAACCTCTACTTTACTTTTTATACCGTCATGGCTGGAAACTAAGTT
> TTT
> >AAGATTTTTCTGGGGTTCCCTTGGCCGAGGTGGGGAGTGGGAGGGCTGTCCAGTGGT
> AGG
> >GACTTAGGATTTTTAGTTTACAGTAGTAGGGGAAACACTCTGTAATCTAATACATAA
> GTA
> >AATGATGTATTAGAATATGGTAAATATAGGCAAGTAGACCCCCACTGGGATTAGCAG
> TGG
> >TGGAAATGTGAGAGAGGGCAAACAGGTGGGTCTAGATGAGGTGTGAGCAGACTCGAG
> GGG
> >CACAGGAGTTAGTCAAGCCAGTATCTGGGGGATAGTGCAGGAATAGTGAACAGCTAG
> ACA
> >AAAAGTCCTAGGGCCAGAGAAAGCAAAAGCATAAGAGATGGAGGCCAGAGAGGTAAT
> CTG
> >GGTGGAAGGCTGCAGCCTCTCAGGATCCCTATAGGTGCTTTGGCTTTTGTTGGAGAG
> ACA
> >CTGAACAGCTTTGGGCAGTGAACGTACCTGACAGGTTTCCTGTTTGTTTTTGAGATG
> AAG
> >TCTCGCTCTTGTCCCCCAGGCTGGAGTGCAATAGCGCGATCTCAGCTCACTGCAACC
> TCT
> >GCCTCCTGTGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAGGTAGCTGGGATTATAG
> GCG
> >CCTGCCACCATGCCTGGCTAATTTTTGTATTTTTAGTAGAGACGCAGTTTCAGCATG
> TTG
> >GCCAGGCTGGTCTTGAACTCCAGACCTCAGGTGATCCGCCCGCCTTGGCCTCCCAAA
> GTG
> >CTGGGATTACAGGCATGAGCCACCGCGCTCGGCTAGACCTGACAGGTTTTAAAAGGA
> TTA
> >CTGGTTGCTGTGTTAAAACAGACTGCAGGATGGCTTAGGTAGCCAGTAGGTTTTTTT
> TTT
> >TTTTTGGAGACGTAGTCTTGCTCTGTTGGCCTGGCTGGAGTGCAGCGGTGTCATCTT
> GGC
> >TCACTGCAAACTCCGCTTCCCGGGTTCAAGTGATTCTCCTGCCTCAGCCTCCGGAGT
> AGT
> >TGGGACTACAGGCGCCCACCACCACACTCGGCTTTTTTGTATTTTTAGTAGAGACGG
> GTT
> >TCACCATGTTGGCCAGGATGGTCTCGATCTCTTGACCTCGTGATCCACCCGCCTTGG
> CCT
> >CCCAAAGTGTTGCGATTACAGGCGTGAGCCACCACGCCTGGACGGGTAGCCAGTAGT
> TTC
> >TAGGGCTGGAGAGATCTAGGATGAGAGAAGTTTCCACATTCCTGTTACAGGCTCTCT
> AAG
> >GCTTCAGCTCCTTTTTCTAGGACTAAGCTGGATCTCAAGTAAACACTAGAGAGGGGG
> CAG
> >CTGAAGCTCCAGGAGTGTGTGGGGCTCCCTGGGGCTGGATGGCGGTGGCGGGCAGGC
> GAG
> >CTGGGCTGTGCTCGGGTGTGTTACAGTAAAGACGCCCAGCTTGGCGCTGGCCCGGCC
> TTT
> >TCACGGTTTTAGGCTCTACAGAGAGCGGCTGCAGAGCTCACCCGGCTGGCAGGAGCC
> ACC
> >GAGGCCGGACACGTGGGCGACTTATTGACCAAGTGGGGAGGAAGCAGCCCCGCACTG
> CTC
> >TCCCGACTGCGGACCACCGTTGGGCTCCTGCGCATCCTAAGCCCCACCGCCTCACCT
> CCA
> >GTCCCCACAGCGTTCGCGCTCCCAGCCGGGGTAAGCGGAAGAAAACAAAGGCCCGGC
> TCC
> >ATCAGGGCACCAATCCCGCTCGTCGGCCTCTTTCTCGGCCTCCAATGAGCTTCTAGA
> GTG
> >TTATCACGCCAGTCTCCTTCCGCGACTGATTGGCCGGGGTCTTCCTAGTGTGAGCGG
> CCC
> >TGGCCAATCAGCGCCCGTCAGCCCACCCCACGAGGCCGCAGCTAGCCCCGCTGGCGG
> CCG
> >AGGCCGGTTGAAGTGGGCGGAGCGGCGGGCGGGGCGTCGCCGTACTAGGCCTGCCCC
> CTG
> >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
> >>
> >>
> >
> >_______________________________________________
> >MOBY-dev mailing list
> >MOBY-dev at biomoby.org
> >http://www.biomoby.org/mailman/listinfo/moby-dev
> >
> >
> >
>
>
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