[MOBY-dev] non-compliant services

[Arnaud Kerhornou]

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
>
>  
>