[MOBY-dev] non-compliant services

[Edward Kawas]

Hi,

Can you send me the workflow and example inputs? 

BTW, the xml looks fine to me.

Eddie

> -----Original Message-----
> From: moby-dev-bounces at biomoby.org 
> [mailto:moby-dev-bounces at biomoby.org] On Behalf Of Arnaud Kerhornou
> Sent: Tuesday, February 14, 2006 9:28 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] non-compliant services
> 
> Hi everyone,
> 
> On this note, I have a service that generates GFF objects, e.g.
> <moby:GFF namespace="" id="ENSBTAG00000014911">
>     <String namespace="" id="" articleName="content">
>     <![CDATA[
>     ENSBTAG00000014911    MatScan    I$HSF_01    490    494   
>   4.99    
> -    .    # AGAAG
>     ENSBTAG00000014911    MatScan    I$HSF_01    487    491   
>   5.48    
> -    .    # AGAAA
>     ]]>
>     </String>
> </moby:GFF>
> 
> Is this object correct. If so would taverna (v1.3.1) be 
> affected by the new object specifications ?
> 
> I have a workflow that connects the output port of a service 
> returning a collection of GFF objects, and feeds a 
> parse_moby_data local processor with this list of simples and 
> when i have GFF objects as above, i get a list of empty objects.
> 
> Thanks
> Arnaud
> 
> Martin Senger wrote:
> 
> >I wonder (I forgot it) what was the decision, after the big change 
> >regarding not inheriting from primitive types,  what to do and when 
> >with services that do not comply with the new specification. I think 
> >that the discussion was about what to do with old data 
> types, there was 
> >even a script to rectify them semi-automatically, but I do 
> not recall 
> >what we said about the services.
> >   An example is a service getFASTAFromUniprot - a nice, 
> fast, possibly 
> >reliable and important service, but it returns something like this:
> >
> ><?xml version='1.0' encoding='UTF-8'?><moby:MOBY 
> >xmlns:moby='http://www.biomoby.org/moby'
> >xmlns='http://www.biomoby.org/moby'><moby:mobyContent
> >moby:authority='mmb.pcb.ub.es'>
> >        <moby:mobyData moby:queryID='sip_1_'>
> >            <moby:Simple moby:articleName=''><FASTA namespace=''
> >id='Q7T7Q6'><![CDATA[&gt;Q7T7Q6_9REOV (Q7T7Q6) Sigma C (Fragment) 
> >AGLNPSQRREVVSLILSLTSNVTISHGDLTPIYERLTNLEASTELLHRSISDISTTVSNI
> >SASLQDMTHTLDDVTANLDGLRTTVTALQDSVSILSTNVTDLTNTSSAHAATLSSLQTTV
> >DGNSTAISNLKSDVSSNGLAITDLQDRVKSLESTASHGLSFSPPLSVADGVVSLDMDPYF
> >CSQRVSLTSYPAEAQLMQFRWMARGTNGSSDTIDMTVNAHCHGRRTDYMMSSTGNLTVTS
> >NVVLLTFDLSDITHIPSDLARLVPSAGFQAASFPVDVSFTRDSATHAYQAYGVYSSSRVF
> >TITFPTGGDGTA
> >]]></FASTA></moby:Simple>
> >        </moby:mobyData>
> >        </moby:mobyContent></moby:MOBY>
> >
> >which is, according my limited knowledge wrong (the FASTA 
> should have a 
> >String with the value there).
> >
> >   Are we going to remove one day such services from a registry?
> >
> >   Cheers,
> >   Martin
> >
> >  
> >
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-dev