Re: [Taverna-users] xml splitter

[Ian D. <Ian...@ma...>]

Hello,

The good/bad news is that the T2 beta replicates this behaviour. So, I  
guess that means it is something in the xml splitters rather than in  
the data layer.  It's good to find these things out early!

Cheers,

Ian

Quoting Alexandra Nenadic <ane...@cs...>:

> Hi,
>
> Got the same results as you - the url element seem empty, even though
> all intermediate results seem fine. We'll have a look into this and get
> back to you.
>
> Regards,
> Alex
>
> Thomas Kelder wrote:
>> Hello,
>>
>> I'm trying to build a workflow that uses WikiPathways, based on the
>> WSDL at http://www.wikipathways.org/wpi/webservice/webservice.php?wsdl.
>>
>> The workflow takes a gene or protein id (e.g. a uniprot id) and calls
>> the 'findPathwaysByXref' function on WikiPathways to find all pathways
>> that contain this protein. To extract the pathway url from the xml
>> response, I use an xml splitter, but this doesn't seem to read the
>> values from the xml correctly.
>>
>> The raw xml response for a single result looks like this:
>>
>> <ns1:result xmlns:ns1="http://www.wso2.org/php/xsd">
>>     <ns2:score xmlns:ns2="http://www.wikipathways.org/webservice">
>>         0.719581081052
>>     </ns2:score>
>>     <ns2:fields xmlns:ns2="http://www.wikipathways.org/webservice">
>>         <ns2:name>graphId</ns2:name>
>>         <ns2:values>cbf</ns2:values>
>>     </ns2:fields>
>>     <ns2:url xmlns:ns2="http://www.wikipathways.org/webservice">
>>
>> http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Apoptosis
>>     </nn2:url>
>>     <ns2:name xmlns:ns2="http://www.wikipathways.org/webservice">
>>         Apoptosis
>>     </ns2:name>
>>     <ns2:species xmlns:ns2="http://www.wikipathways.org/webservice">
>>         Homo sapiens
>>     </ns2:species>
>>     <ns2:revision xmlns:ns2="http://www.wikipathways.org/webservice">
>>         15853
>>     </ns2:revision>
>> </ns1:result>
>>
>> I'm connecting the 'url' output of the xml-splitter to a workflow
>> output. In the results tab, I see a list with results (the number of
>> elements corresponds to the number of pathways found), but the values
>> seem empty.
>>
>> The workflow to reproduce this problem can be downloaded here:
>> http://ftp2.bigcat.unimaas.nl/~thomas.kelder/get-pathways-by-xref.xml
>> <http://ftp2.bigcat.unimaas.nl/%7Ethomas.kelder/get-pathways-by-xref.xml>
>>
>> Does anyone have an idea on how I can figure out what's wrong?
>>
>> Thanks a lot!
>> Thomas
>>
>> ------------------------------
>> Thomas Kelder, MSc.
>> BiGCaT Bioinformatics
>> Universiteit Maastricht
>> P.O. Box 616, 6200 MD Maastricht
>> Phone:  +31 (0)43 3882913
>> Email:   tho...@bi...
>> <mailto:tho...@bi...>
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>
> --
> .....................................
> Dr Alexandra Nenadic
> Research Associate, myGrid Project
> School of Computer Science
> University of Manchester
> Web: http://www.cs.man.ac.uk/~nenadic
> Office: +44 (0)161 275 0672
> Fax: +44 (0) 161 275 6204
>
>
>
>
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> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
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> _______________________________________________
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> Documentation: http://www.mygrid.org.uk/usermanual1.7/
> FAQ: http://www.mygrid.org.uk/wiki/Mygrid/TavernaFaq
> Biological Services:   
> http://www.mygrid.org.uk/wiki/Mygrid/BiologicalWebServices
>