[Taverna-users] WSDL empty parameters issue - PICR 'getUPIForSequence' webservice

Thu, 14 Oct 2010 09:47:14 -0700 

 Hi dear all.
I'm on to upgrading to T2.2 from T1.7.2. In older version, I used "EBI_PICR_Sequence_to_UniParc_and_InterPro <http://www.myexperiment.org/workflows/235.html>" workflow without any problem. I'm not able to make it running correctly in T2.2, the difference seems to be in parameters sent to 'getUPIForSequence' webservice. 

In taverna 1.7.2 it was:

<parameters 
xmlns="http://www.ebi.ac.uk/picr/AccessionMappingService";><sequence>&gt;Swiss-Prot|P24631

MDGRMFGLETPLMVALQHLLDVPDGDAGAGGDKAGGGGPTRTYVADARAMAVTPADVKELPGAYAFVVDMPGLGTGDIKVQVEDERVLVISGERRREEREDAKYLRMERRMGKFMRKFVLPDNADMDKISAVCRDGVLTVTVEKLPPPEPKKPKTIEVKVA</sequence></parameters>

In taverna 2.2, it is:

<parameters 
xmlns="http://www.ebi.ac.uk/picr/AccessionMappingService";><sequence>&gt;Swiss-Prot|P24631

MDGRMFGLETPLMVALQHLLDVPDGDAGAGGDKAGGGGPTRTYVADARAMAVTPADVKELPGAYAFVVDMPGLGTGDIKVQVEDERVLVISGERRREEREDAKYLRMERRMGKFMRKFVLPDNADMDKISAVCRDGVLTVTVEKLPPPEPKKPKTIEVKVA</sequence><searchDatabases></searchDatabases><taxonId></taxonId><onlyActive></onlyActive></parameters>


Empty parameters are sent, and apparently the webservice is not able to 
process them correctly, result is empty - while T1.7.2 succeeded (cf 
attached result file):

<getUPIForSequenceReturn />

Is this a known issue?

Is it possible to make the workflow running by deleting parameters from 
'PICR_input_params' in Taverna? I took a look, but did not find how to 
do so.


Thanks for help.

Regards.

--
Raphaël Flores
Téléphone : 01 69 33 23 56
UMR de Génétique Végétale, INRA, Univ. Paris-Sud, CNRS, AgroParisTech,
F-91190 Gif-sur-Yvette, France


<getUPIForSequenceReturn 
xmlns="http://www.ebi.ac.uk/picr/AccessionMappingService"; 
containsActiveSPTRCrossReference="true"><ns2:CRC64 
xmlns:ns2="http://model.picr.ebi.ac.uk";>3E60A8DD4396577C</ns2:CRC64><ns2:UPI 
xmlns:ns2="http://model.picr.ebi.ac.uk";>UPI000012CC06</ns2:UPI><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>P24631</ns2:accession><ns2:accessionVersion>1</ns2:accessionVersion><ns2:databaseDescription>UniProtKB/Swiss-Prot</ns2:databaseDescription><ns2:databaseName>SWISSPROT</ns2:databaseName><ns2:dateAdded>1992-03-01T00:00:00.000Z</ns2:dateAdded><ns2:dateDeleted>2010-11-02T00:00:00.000Z</ns2:dateDeleted><ns2:deleted>false</ns2:deleted><ns2:gi>123549</ns2:gi><ns2:taxonId>4577</ns2:taxonId></ns2:identicalCrossReferences><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>HC702313</ns2:accession><ns2:accessionVersion>1</ns2:accessionVersion><ns2:databaseDescription>European
 Patent 
Office</ns2:databaseDescription><ns2:databaseName>EPO</ns2:databaseName><ns2:dateAdded>2010-06-10T00:00:00.000+01:00</ns2:dateAdded><ns2:dateDeleted>2010-09-11T00:00:00.000+01:00</ns2:dateDeleted><ns2:deleted>false</ns2:deleted><ns2:gi
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:taxonId>4577</ns2:taxonId></ns2:identicalCrossReferences><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>1805370B</ns2:accession><ns2:accessionVersion
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:databaseDescription>Protein Research 
Foundation</ns2:databaseDescription><ns2:databaseName>PRF</ns2:databaseName><ns2:dateAdded>2005-11-28T00:00:00.000Z</ns2:dateAdded><ns2:dateDeleted>2009-09-01T00:00:00.000+01:00</ns2:dateDeleted><ns2:deleted>false</ns2:deleted><ns2:gi
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:taxonId>4577</ns2:taxonId></ns2:identicalCrossReferences><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>S14998</ns2:accession><ns2:accessionVersion
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:databaseDescription>PIR-PSD</ns2:databaseDescription><ns2:databaseName>PIR</ns2:databaseName><ns2:dateAdded>2003-04-11T00:00:00.000+01:00</ns2:dateAdded><ns2:dateDeleted>2005-01-04T00:00:00.000Z</ns2:dateDeleted><ns2:deleted>true</ns2:deleted><ns2:gi
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:taxonId xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; 
xsi:nil="true" /></ns2:identicalCrossReferences><ns2:identicalCrossReferences 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>CAA38013</ns2:accession><ns2:accessionVersion>1</ns2:accessionVersion><ns2:databaseDescription>EMBL
 Nucleotide Sequence 
Database</ns2:databaseDescription><ns2:databaseName>EMBL</ns2:databaseName><ns2:dateAdded>2003-03-12T00:00:00.000Z</ns2:dateAdded><ns2:dateDeleted>2010-09-10T00:00:00.000+01:00</ns2:dateDeleted><ns2:deleted>false</ns2:deleted><ns2:gi>22339</ns2:gi><ns2:taxonId>4577</ns2:taxonId></ns2:identicalCrossReferences><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>NP_001105705</ns2:accession><ns2:accessionVersion>1</ns2:accessionVersion><ns2:databaseDescription>RefSeq
 release + 
updates</ns2:databaseDescription><ns2:databaseName>REFSEQ</ns2:databaseName><ns2:dateAdded>2007-12-15T00:00:00.000Z</ns2:dateAdded><ns2:dateDeleted>2010-09-15T00:00:00.000+01:00</ns2:dateDeleted><ns2:deleted>false</ns2:deleted><ns2:gi>162463382</ns2:gi><ns2:taxonId>4577</ns2:taxonId></ns2:identicalCrossReferences><ns2:identicalCrossReferences
 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>S14998</ns2:accession><ns2:accessionVersion
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:databaseDescription>PIR-PSD 
archive</ns2:databaseDescription><ns2:databaseName>PIRARC</ns2:databaseName><ns2:dateAdded>2003-03-31T00:00:00.000+01:00</ns2:dateAdded><ns2:dateDeleted>2003-04-04T00:00:00.000+01:00</ns2:dateDeleted><ns2:deleted>true</ns2:deleted><ns2:gi
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:taxonId xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; 
xsi:nil="true" /></ns2:identicalCrossReferences><ns2:logicalCrossReferences 
xmlns:ns2="http://model.picr.ebi.ac.uk";><ns2:accession>HSP21_MAIZE</ns2:accession><ns2:accessionVersion
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:databaseDescription>SWISSPROT</ns2:databaseDescription><ns2:databaseName>SWISSPROT</ns2:databaseName><ns2:dateAdded
 xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:dateDeleted xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; 
xsi:nil="true" /><ns2:deleted>false</ns2:deleted><ns2:gi 
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:nil="true" 
/><ns2:taxonId>4577</ns2:taxonId></ns2:logicalCrossReferences><ns2:sequence 
xmlns:ns2="http://model.picr.ebi.ac.uk";>MDGRMFGLETPLMVALQHLLDVPDGDAGAGGDKAGGGGPTRTYVADARAMAVTPADVKELPGAYAFVVDMPGLGTGDIKVQVEDERVLVISGERRREEREDAKYLRMERRMGKFMRKFVLPDNADMDKISAVCRDGVLTVTVEKLPPPEPKKPKTIEVKVA</ns2:sequence><ns2:timestamp
 
xmlns:ns2="http://model.picr.ebi.ac.uk";>2009-01-12T00:00:00.000Z</ns2:timestamp></getUPIForSequenceReturn>
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