[MOBY-dev] Updates to MOBY Central and IMPORTANT NOTES for registry hosts

[Mark Wilkinson]

ALSO NOTE!  The MOBY Central daemon code has changed in two lines - see  
moby-live/Perl/scripts/MOBY-Central.pl for the new code.

M



On Mon, 05 Feb 2007 20:02:03 -0800, Mark Wilkinson <markw at illuminae.com>  
wrote:

> Hi all,
>
> First off, apologies to anyone who was trying to get through to MOBY  
> Central this afternoon - Eddie and I were making the changes necessary  
> to get it ready for SOAP::Lite 0.69 and the changes that worked  
> perfectly on the test server didn't work on the real MOBY Central... so  
> it took a couple of hours of troubleshooting before we had it back up  
> again.
>
> The good news is that it seems to work correctly with both Perl and Java  
> clients.  What we don't know is if it is backwards compatible with  
> earlier versions of the MOBY::Client::* libraries, in particular,  
> MOBY::Client::Service.  I *think* it is, but we didn't have the  
> opportunity to test it.  In any case, the API did not change, so if you  
> just cvs update your client libraries everything should come back to  
> life if it isn't working.
>
> Upgrading to SOAP::Lite 0.69 was a nightmare!  The new SOAP::Lite  
> behaves subtly differently than the old one in several ways that we were  
> not expecting.  Thankfully, Pieter and Eddie had done most of the  
> trouble-shoting already, but it still threw us for a loop in some places  
> with incompatible SOAP version errors and a new auto-encoding of strings  
> by SOAP::Lite that we used to do in-code by ourselves (resulting in  
> double-coded messages).
>
> Anyway, it's done now.  Please scream loudly if it doesn't work for  
> you!!  I have backups of everything so if necessary we can roll-back  
> quickly.
>
> All of this was done primarily to get us to be compatible with the new  
> Asynchronous services API that use the Manchester WSRF::Lite modules  
> which depend on SOAP::Lite 0.69.  Can I ask the good folks at INB to  
> test the code to see if it works for them v.v. Async services?  The  
> database can now hold Category=moby-async (which reminds me, I need to  
> update the database templates in the CVS...), and Eddie assures me that  
> the code will now provide correct WSDL for an Asych interface.  The  
> myGrid folks have added moby-async as a valid service category into  
> their ontology as well, so in principle... it should all work... (touch  
> wood!)
>
> *********************
> IMPORTANTLY this means that the new MOBY Central code will likely NOT  
> work on versions of SOAP::Lite prior to 0.69!!!  Keep this in mind if  
> you are running your own registry...
> *********************
>
> Tomorrow (if I have regained my sanity after todays hell ;-) ) I'll try  
> to make the changes to gbrowse_moby such that it can also invoke  
> asynchronous services.  I think the Async modules also need to be added  
> to the MANIFEST before they are installed by default, so I'll try to  
> remember to do that as well.
>
> Otherwise there were just some small changes to the test suite to better  
> clean-up the registry if something goes wrong during testing, and I  
> cleaned-up the test database so that it also doesn't cause the test  
> suite to fail.  I will restart the test registry using the new codebase  
> first thing in the morning so that the two are identical.
>
> We still haven't figured out why those namespace changes happened a  
> couple of days ago.  It coincided with the Gene Ontology curators making  
> some additions to the Namespace list, so I suspect that there is a bug  
> in the interface I have given to them (which talks directly to the  
> database without using the MOBY API), but exactly WHY this happened is  
> still a mystery.  I've alerted Midori to the problem and she's going to  
> hold-off on making any more changes until we can figure out what is  
> going wrong.
>
> That's all the news from MOBY Central!
>
> Let us know ASAP if you notice anything wrong.  It's been a rough ride  
> today...
>
> Mark
>



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