[MOBY-dev] Migrating MOBY Central to the new object API - MONDAY OCT 24th

[Mark Wilkinson]

Hi all, 

Eddie and I have been discussing the object ontology migration now that
we are not allowing inheritance from primitives.  No matter what we do
this will break some services, and though I was originally hoping to
soften the blow by having a deprecation period, the amount of pain this
causes (i.e. everyone having to edit and re-register their services
TWICE!) is just inhumane :-)

So... I am sure that some of you will cheer this decision, and others
will loathe it... we're going to simply migrate the object ontology (in
the public MOBY Central here at iCAPTURE) with **no deprecation period
at all**.  

The object names will remain exactly as they are, but will (in some
cases) now have different definitions.  As such, for those of you
running services that are affected by this change, you will only need to
update your service code, but NOT need to de/re-register your service.

We plan to do this Monday October 24th, so you have a few days to update
your services now to reduce the down-time.  The way to go about updating
your services is as follows:  Any XML node that currently has content,
but is not a nominal primitive, will now be modified such that it
CONTAINS a node that is a primitive, and that primitive will have data
content.  It's articleName is "content" in every case.  

e.g.  

  <FASTA namespace='' id=''><![CDATA[
     >name
     ACGTGTAGTGCTAGTC
   ]]></FASTA>

will become

   <FASTA  namespace='' id=''>
	<String namespace='' id='' articleName='content'><![CDATA[
		>name
                ACGTGTGCTGATGAC
	]]></String>
   </FASTA>


And similarly for Integers, Floats, DateTime, etc.  The definition of
DateTime will also change, such that it is a primitive, rather than
inheriting from String, as it currently does.

Eddie has a migration script that will update your mySQL databases
automatically.  He will make this available on his website (details to
follow).


Any objections?  (don't all yell at once ;-) )

Cheers!

Mark



-- 
"Ontologists do it with the edges!"

Mark Wilkinson
Asst. Professor
Dept. of Medical Genetics
University of British Columbia
PI in Bioinformatics
iCAPTURE Centre
St. Paul's Hospital
Rm. 166, 1081 Burrard St.
Vancouver, BC, V6Z 1Y6
tel: 604 682 2344 x62129
fax: 604 806 9274