[MOBY-dev] 0.85 codebase running on test server

[Mark Wilkinson]

Hi dev-ers

Anyone watching the commit logs will have seen a lot of activity in the
past week!

The 0.85 codebase is running now on a test server so that you can start
to code to it.  Endpoint information is as follows:

URL => 'http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-
Central.pl',
URI => 'http://bioinfo.icapture.ubc.ca/MOBY/Central

The main (visible) difference is that many of the messages now contain
LSID information - see the 0.85 API on the biomoby.org website for full
details.  In addition the use of LSID's in MOBY Central messages should
be MUCH more consistent now.  The LSID resolver is (should be!) working,
so if you try to resolve those LSID's to metadata you will get useful
information.

Under the hood, Dennis Wang has factored out all of the data-access
calls into a single adaptor module (good job Dennis!).  Hopefully this
will simplify our migration toward the myGrid registry, since we will
only need to modify one module.

heads-up that Eddie is working on this same test server with the RDF
agent, so things you register there may not last for long as they are
obliterated by agent activity (and bugs ;-) ), but the MOBY Central code
(what is currently in the CVS) seems to be running correctly on that
machine so you can at least use it to observe the new message structure
and update your code if necessary in anticipation of the production
server switching to this codebase.

If you have time/ambition/interest please do test this code and let me
know if you notice anything incorrect.  

One of the biggest improvements, in my opinion, is that there is now a
very comprehensive test suite for the Perl code - 122 tests!  (up from
just 12 before).  All tests pass on two of my servers, so I think the
code is now ~stable.  From here on, any bugs that are reported will be
fixed together with an addition to the test suite to make sure they
don't reappear.  As such, the codebase should never degrade again :-)
Yes, we're growing up and becoming a mature project!  Nota Bene that the
test suite DOES NOT PASS ALL TESTS against the current production
registry (@mobycentral.icapture.ubc.ca).  This is because there are some
latent bugs in the current production code that are now revealed by the
test suite!!

That's all the news.

In the pipeline:  

1)  I will soon commit code changes that prevent inheritance from
Primitives
2)  I'll create and register replacement objects for all objects that
currently inherit from primitives such that they follow the paradigm for
object construction that has been extensively discussed since the last
meeting.
	2a) I will attempt to contact all service providers who will be
affected by this change based on their registered contactEmail address
3)  Eddie has a test suite of ~50 tests for the RDF agent, however it is
not yet passing all tests.  Once we believe this is stable/safe we will
switch it on and from that point onwards deregistration of services will
occur only through agent activity.
4)  We are assembling a thesaurus of RDF predicates for service
providers to use in their service instance metadata.  This will be
published shortly.

Eddie and I leave for 10 days in Manchester on Sunday, so hopefully
there will be more news and progress by the time we get home.

Cheers everyone!

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