[Biocorba-l] Re: cvs.bioperl.org running ensembl perl corba

[Brad Chapman]

Hi Jason;
Thanks for moving this to biocorba-l!

> Some other issues we are having - versions of ORBit > 0.5.3 (Brad - remind
> us?)  are not playing nicely with CORBA::ORBit perl module.  

Okay, I think I got this all figured out last night. The problem isn't 
with CORBA::ORBit, the problem is with interoperability with other
ORBs. ORBit versions >= 0.5.3 don't produce IIOP messages by
default. The ORBit FAQ:

http://orbit-resource.sourceforge.net/faq.html

indicates that this is due to security concerns. So by default ORBit
will only produce messages that ORBit can read. The flag ORBIIOPIPv4=1 
allows ORBit to produce valid IIOP that other ORBs can
read. Putting this into /etc/orbitrc clears everything up and there
are not interoperability concerns. ORBIIOPIPv4 specifies IIOP version
1.0, which is the standard, and ORBIIOPIPv6 specifies IIOP version
1.1, which I'm not positive is widely supported. So at least for me,
sticking the v4 flag in there seems to clear up all concerns, so ORBit 
0.5.7 works okay. Whew, so anyways, that's what I know.

I don't know about ORBit-mt and how that'll work -- I haven't tried it 
yet.

> Brad - reason code is still complaing about Obj cvs DBAdaptor code is the
> ensembl code on cvs.bioperl is from the anonymous repository and it wasn't
> updated immedietly after I checked into ensembl - will do a cvs update this
> morning and restart server -- suspect that will set things right.
[...later...]
> Brad - I updated server code and ensembl cvs code.  Obj -> DBAdaptor msgs
> should be going away (had to update the server perl script as well)

Hmm, it looks like there are still some issues with differences
between object and DBAdapter. The one I saw so far (which stops me
from testing more):

--> EnsemblFactory::get_GeneFactory:
Error occured in implementation 
'Bio::EnsEMBL::CORBA::EnsemblFactory::get_GeneFactory': 
Can't locate object method "get_Gene_Obj" via package 
"Bio::EnsEMBL::DBSQL::DBAdaptor" at 
/home/jason/ensembl/src/ensembl-corba-server/modules/Bio/
EnsEMBL/CORBA/EnsemblFactory.pm line 107.

==> After digging through DBAdaptor (damn, that's a big module!), it
seems like the function is called 'gene_Obj' now.

Don't know if that'll fix everything but it's a start. Talk with you
soon.

Brad