[Biocorba-l] Bioperl biocorba server code checked in

Sat, 10 Feb 2001 08:50:00 -0500 (EST)

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[patches for bugs]
> Feel free to send them on-list ;) - I am hacking biocorba-server at the
> moment (between gene builds/assembly shit over at Ensembl) and would be
> happy to fix them...

Okee dokee :-). Below is the buffer that describes the changes I
fixed, and the stuff I found I couldn't fix. Six patches are also
attached. Thanks for checking this out.

> I'd love to see biopython/bioperl (and biojava for that
> matter) interoperability in-real-life...

I have been using biocorba to go between Biopython and Bioperl quite a 
bit in my research (if you can call my research real life :-). Have
been using a Bioperl SeqDB server to hold the Arabidopsis genome, and
been messing with it from there. The code is at:

http://www.bioinformatics.org/bradstuff/brad-moinmoin/moin.cgi/PgmlLibrary

if you are really into it. Most of the biocorba stuff needs an update
-- I'll hopefully be doing that soon now that I am going to have a
server that I can use :-)

Brad

Bug Buffer
==========
Fixed
-----
* PrimarySeq::subseq -- was trying to check max_request_length, but 
there wasn't any such thing. Just defined an internal hash value for
it, set to some arbitrary big number like 1Mb. 

* PrimarySeqDB::version -- getting seg-faults when trying to call
this. Problem was a reference to seqdb, instead of _seqdb. Also, the
database tries to return a version like 0.2, but it can't do this since
only longs are defined, so zero is always returned.

* PrimarySeqDB::get_PrimarySeq -- has the same problem with referencing
seqdb instead of _seqdb.

* PrimarySeqDB::get_PrimarySeq again -- There also doesn't seem to be
a function in the Bio::Index stuff to get a PrimarySeq directly from an
id. Instead, I got the Seq, and then got a primary seq from this.

* PrimarySeq::get_SeqFeatures_in_region_by_type -- Complaints about
Bio::Range not having a "new". Fixed by including use Bio::Range;

* SeqFeatureIterator::next -- wasn't checking for EndOfStream;

* SeqFeatureVector::elementAt -- wasn't turning the bioperl SeqFeature
object into a biocorba SeqFeature object.

* Seq::get_SeqFeatures_in_region[_by_type] -- was raising
UnableToProcess errors instead of OutOfRange errors.

* Seq::get_SeqFeatures_in_region[_by_type] -- trying to use 
range->contains on a SeqFeature object and not a range object. Changed
to create a range for the SeqFeature, and then check.

Not fixed
---------
* Seq::get_SeqFeatures_in_region/by_type -- All of these functions first
make a call to all_Features, which retrieves BioCorba objects, and not
bioperl objects. Then when you try to get a SeqFeature out of a Vector 
or Iterator created with these objects, the SeqFeature constructor will
die with: "Must have poa and seq into Seq Feature." I didn't want to get
too into this, since this would involve rewriting parts of these 
implementations -- I'm not sure about the best way to handle it.

* PrimarySeq/AnonymousSeq implementation -- one issue with the way you
implemented these as one class is that if a client tries to narrow a
PrimarySeq object to the AnonymousSeq interface (which it should be able
to do), the server will die since it has no AnonymousSeq implementation
to narrow to. The solution to this would be to implement AnonymousSeq
separately and then inherit from it with PrimarySeq.

* Unknown::query_interface -- Anything I do here causes the server to 
crash :-<. If you try to return anything but a CORBA::Object, ORBit
will complain about having problems marshalling the object, and if you
try to return a CORBA::Object, the server seg-faults. I don't know what
to do to just keep this from blowing up. Any thoughts?

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