[MOBY] RE: [MOBY-l] Problem invoking services

Mon Oct 13 14:23:58 EDT 2003

Hmm...

Ok, I've modified the XML, to the following:
<?xml version="1.0" encoding="UTF-8"?>
<soapenv:Envelope xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
 <soapenv:Body>
  <namesp3:getGoTermService xmlns:namesp3="http://biomoby.org/">
  <body>
   <![CDATA[<?xml version='1.0' encoding='UTF-8'?>
<moby:MOBY xmlns:moby='<http://www.biomoby.org/moby-s'>>
	<moby:Query>
		<moby:queryInput moby:articleName=''>
			<moby:Simple>
				<Object namespace="GO" id="GO:0008303" />
			</moby:Simple>
		</moby:queryInput>
	</moby:Query>
</moby:MOBY>]]>
  </body>
    </namesp3:getGoTermService>
 </soapenv:Body>
</soapenv:Envelope>

So, the Object line looks as it does in the API examples. However, I'm still
getting back responses with nothing in them. Am I doing something else
wrong? I THINK the GO id is correct, because it works when I run it through
the web-based moby client at
http://mobycentral.cbr.nrc.ca/cgi-bin/Client/MOBY-Client05.cgi

Any ideas about what's going wrong now?

Jay Potts
Software Engineer / AI Specialist
Discovery Machine Inc.
www.discoverymachine.com

"Every artist must have two fears--
the fear of God and the fear of man--
fear of God that his creation will ultimately be found unworthy
and the fear of man that he will be misunderstood by his fellows."
- Robert Frost

-----Original Message-----
From: Mark Wilkinson [mailto:markw at illuminae.com]
Sent: Monday, October 13, 2003 12:16 PM
To: Jay Potts
Cc: Martin Senger; Ken Steube; mobyl
Subject: Re: [MOBY] RE: [MOBY-l] Problem invoking services

:-)  You're ALMOST there!

Put your XML into a validator to discover the problem ;-)

(hint... you missed the closing tag on Object)

Just FYI - one of the decisions that we made at the meeting last weekend
was that, by convention, we will no longer allow ID numbers to be
prefixed with their namespace, so as soon as I update my service it will
no longer accept "GO:0003463" but only "0003463" as the ID field.  This
is because everyone uses a different convention for prefixing (e.g.
GO:0001234, gi|123456) so it is best to disallow it completely since we
break out the namespace component anyway.

As soon as I can find a couple of hours free I will write up the minutes
and update the API with the changes we made on the weekend.

M

On Mon, 2003-10-13 at 09:45, Jay Potts wrote:
> Hey Folks,
> I think I'm getting a little closer to being able to query services,
however
> I'm still running into a few problems. Although, at this point I think
it's
> a question of sending the correct data. I'm a software engineer, and not a
> biologist, so I'm not exactly sure what most of these services do. :)
> Anyway, I'm trying to access the getGoTerm service.
> I've constructed the following message:
> <?xml version="1.0" encoding="UTF-8"?>
> <soapenv:Envelope
xmlns:soapenv="http://schemas.xmlsoap.org/soap/envelope/"
> xmlns:xsd="http://www.w3.org/2001/XMLSchema"
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
>  <soapenv:Body>
>   <namesp3:getGoTermService xmlns:namesp3="http://biomoby.org/">
>   <body>
>    <![CDATA[<?xml version='1.0' encoding='UTF-8'?>
> <moby:MOBY xmlns:moby='<http://www.biomoby.org/moby-s'>>
>       <moby:Query>
>               <moby:queryInput moby:articleName='ccc'>
>                       <moby:Simple> <Object namespace="GO" id="GO:0008303"
> </moby:Simple>
>               </moby:queryInput>
>       </moby:Query>
> </moby:MOBY>]]>
>   </body>
>     </namesp3:getGoTermService>
>  </soapenv:Body>
> </soapenv:Envelope>
>
> I've sent it to the endpoint:
> http://mobycentral.cbr.nrc.ca/cgi-bin/Services/Services.cgi
> with the namespace: http://biomoby.org/#getGoTerm
>
> I'm able to do this now, without getting any errors or faults. However,
the
> response I get seems to be mostly empty:
> <?xml version='1.0' encoding='UTF-8'?>
>       <moby:MOBY xmlns:moby='http://www.biomoby.org/moby'>
>         <moby:Response moby:authority='http://www.illuminae.com'>
>
>     </moby:Response>
>       </moby:MOBY>
>
> I take this to mean that it's just giving me nothing back, because I sent
in
> the wrong data. Does anyone know from looking at the message I'm sending
> out, what I'm getting wrong? I'm pretty sure that GO id is correct, as I'm
> able to use the little moby client that's up on the web to query it and
get
> a resulting GO_Term back.
>
>
> _______________________________________________
> moby-l mailing list
> moby-l at biomoby.org
> http://biomoby.org/mailman/listinfo/moby-l
--
Mark Wilkinson <markw at illuminae.com>
Illuminae