[Biocorba-l] Bioperl biocorba server code checked in

[Brad Chapman]

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[my bug list from before]

Jason:
> I fixed these bugs.  Brad if you can run your code some more to see if
> this fixes your observed bugs.  I added some more tests to the local
> server/client code to test the different cases of SeqFeature.  I know
> there needs to be more tests and they ought to be done in a nice perl
> manner, I'll see if I can plug away some more later.

Yup, this fixes lots of my problems. Thanks Jason! I worked at this
more and got another list of (smaller) bugs for you. If these get
fixed, then we should have interoperability for just about everything!
Very nice. I checked the test suite into biopython-corba CVS, so if
you (or anyone else) wants to check it out, it is waiting in 
Tests/test_PerlServers.py.

Thanks again for dealing with these bugs for me. Here is the buffer I
kept while working on this latest round of debugging. Proposed patches 
are attached.

Brad

Fixed
-----
* PrimarySeq::primary_id -- Returns a stringified memory location if 
there is not a primary_id, which can make CORBA unhappy (plus it looks
pretty funny to get back a perl hash!). Fixed this, 
but the fix reaches into the internal hash of the PrimarySeq, which
is probably not the best way. Better suggestions are very welcome. 
Now returns "unknown" if no id is set.

* PrimarySeqDB::get_PrimarySeq -- Calls the function 
get_PrimarySeq_by_primary_id, which doesn't appear to actually exist.
Had this problem before, I think the fix just forgot to change the 
function call.

* PrimarySeqVector::elementAt -- Has a problem when created from a
PrimarySeqDB, since the PrimarySeqDB was passing in CorbaServer::Seq objects
and not CorbaServer::PrimarySeq objects. Fixed in PrimarySeqDB.

* PrimarySeqVector::iterator -- This call was not working correctly for
two reasons. First, it passed the items as '-elements' instead of '-items'.
Second, new for PrimarySeqIterator didn't seem to act right if you pass in
a valid list of items (it still was requiring a SeqIO instance).

* BioEnv::get_SeqDB_names -- Was not returning an array reference, 
at least not in the case where there were no sequence databases.

* BioEnv::get_Seq_from_file -- This was segfaulting. One problem was a
call to _get_seqio that didn't exist -- got rid of this.

Not Fixed
---------
* Damn, changing the AnonymousSeq to its own module didn't help with
the problem with narrowing. Sorry :-<. I think we're going to have to
chalk this one up to an interoperability bug. I just changed the 
biopython stuff so that it doesn't ever try to narrow to check interface
inheritance.


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