[MOBY] [MOBY-l] Output of a service

[Mark Wilkinson]

Hi Catherine!

Congratulations on your first service :-)

A few comments, and answers to your questions:


>     serviceType  => "Analysis",

please feel free to register a more descriptive service type that
inherits from "Analysis" - e.g. melting_point_determination ISA Analysis

... though if we were to do it right, it should probably have a bit more
granularity than that... something like:

Nucleotide_Sequence_Analysis
DNA_Sequence_Analysis
Physical   ( Structural...      Chemical...    Functional...)
Melting_Point


>   my @simples = MobyXmlObject->getMobySimples($query);

I see you are using Ken's code to get the Simples.  This is fine, but I
don't think his code has been updated with the recent API changes that
require the inputs to be enumerated.  Ken?  Also, Ken, perhaps you could
migrate these routines into the CommonSubs.pm module (or simply add your
module in the CVS) to make it easier for all of us to keep the code
up-to-date with API changes.

Catherine - you wont *break* anything by being non-compliant in this
way, since these API changes were all backward-compatible, however you
wont be 100% compliant... which is a shame for your first service :-)

>         <text-plain namespace='' id=''>
>             <![CDATA[$textresult]]>
>             </text-plain>

You should probably register an object that inherits from text-formatted
(rather than text-plain) and give it the name of your analysis program
e.g. as we have done with NCBI_Blast_Text and NCBI_Blast_XML.


>     $MOBY_RESPONSE .= simpleResponse($result, '');

simpleResponse now takes three arguments, the third one being the
enumerated identity of the query to which you are responding (see
above).  Again, you wont *break* anything by doing it this way, but...


>   return responseHeader . $MOBY_RESPONSE . responseFooter;

responseHeader also takes arguments.  At a minimum, it takes your
authority, but it can also be used to provide serviceNotes.

responseHeader('bioweb.pasteur.fr');

or

responseHeader(
	-authority => 'bioweb.pasteur.fr', 
	-note => 'software version xxx');

something like that...

> The "debug" step worked ok. Now, it is the ->execute() that returns... nothing.

Unfortunately, I don't see your service in the registry, so you must
have it in some private registry?  If I could see it, I could help you
debug it...

> the XML description associated to an object is.

Ken has this tool in his "encyclopedia":

http://plantsp.sdsc.edu/cgi-bin/MOBY/MOBY_display_object_xml.cgi?obj=PutYourObjectHere

> 1) Do we have to register a sub-class of text-plain or is it possible de use the 
> text-plain object type? 

You can output text-plain if you wish, but it is better "semantically"
to create a specific object type for a specific data type, as this will
help people to e.g. create parsers for your output (parsing "plain-text"
would be meaningless... ;-) )

> 2) If we have to register a new object type :
> 	- a) What kind of namespace would you use for such a new object type then? 

you don't register namespaces together with objects - the two things are
independent.  What you would do is to take the namespace/id from the
incoming request object and use that as the namespace/id of your
outgoing plain-text (or whatever) object.  The way to think of MOBY
Analysis services is that they take incoming data and output a different
representation of the same data, hence the output has the same
namespace/ID as the input (in most cases...)


> 3) Once you know what type of object you have to return, how do you provide it
> as a return value of your service? In raw XML?

Your service code is ~perfect as far as I can see, so I am not sure why
you are not getting any output from it... Your interpretation of the
spec seems to be 100% correct!  

yes, when using the simpleResponse subroutine you do exactly as you say
- you give it raw XML, and it will build the response for you.

> I hope these are not too much FAQ, thanks in advance,

I'm sorry that I wasn't able to solve your exact problem... if you
register your service in the public registry I will play with it today
and we should have it fixed up right away!

Cheers!

M

-- 
Mark Wilkinson (mwilkinson at mrl.ubc.ca)
University of British Columbia iCAPTURE Centre