[Bioperl-l] RE: [BioSQL-l] GBrowse on BioSQL dead in water again

[Hilmar Lapp]

For production work do not use the head of bioperl-db nor biosql-schema. Use the branch bioperl-release-1-1-0 from both modules (I did announce this on both lists). That branch has the API unchanged and the schema only changed where it shouldn't break existing adaptors (if there are changes which do break adaptors, I'll fix this on the branch, unless the adaptor broke because it was using '*' as the select list).

I have yet to re-introduce DAS support into the main trunk. I'd appreciate any help or advice for doing this (what do I need to look at or implement), as it will be helpful for us here as well.

Also, if anyone wants to volunteer taking this on, I'll be more than glad to explain how the adaptors now work. I hesitated doing this on the list yet because I've just started running tests on a larger scale (dumping swissprot now works), and changes may or may not become necessary.

As a brief status report, all tests in t/ pass except for one (test, not script) which tests for DBLink::optional_id, which is unsupported right now. As for the adaptors and schema support, the (subjectively) important parts work. What doesn't work so far comprises of remote locations, fuzzy locations, sub-seqfeatures, ontology relationships, and qualifiers for dbxrefs. That these don't work means the respective information will be lost and not stored; it will not crash a script or report an error.

Also, there is only mysql support for now. I'm going to start porting driver specific code to oracle today or tomorrow. I'll take on Postgres only after that. Again, anyone willing to volunteer is greatly welcome and I'll explain what needs to be done.

On a separate note, be aware that the biosql schema on the main trunk is not fully stable yet. I have a couple more change requests pending that I'll post soon. I'll adapt the bioperl-db adaptors for all of such schema changes.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Tuesday, October 08, 2002 1:16 PM
> To: elia@gugu-sg.org
> Cc: bioperl-l@bio.perl.org; biosql-l@open-bio.org
> Subject: [BioSQL-l] GBrowse on BioSQL dead in water again
> 
> 
> Hi Elia,
> 
> Alas, the latest CVS update of bioperl-db removed the
> Bio::DB::BioSQL::BioDatabaseAdaptor module, and so broke the
> Bio::DB::Das::BioSQL module that was dependent upon it.  There is no
> obvious documentation of what the preferred interface now is.  Could
> you show me how to rewrite the following script for me to use the
> approved API?
> 
> I had been running GBrowse very happily on top of it until now, but
> I'm afraid that it is now dead in the water.
> 
> Thanks,
> 
> Lincoln
> 
> -----------
> 
> #!/usr/bin/perl
> 
> use Bio::DB::BioSQL::BioDatabaseAdaptor;
> use Bio::DB::BioSeqDatabase;
> 
> my $dbc = Bio::DB::BioSQL::BioDatabaseAdaptor->new_from_registry(
> 						    driver   => 'mysql',
> 						    dbname => 'biosql',
> 						    biodbname => 'test',
> 						    host   => 
> 'localhost',
> 						    user   => 'lstein',
> 						    pass   => undef,
> 						    port   => undef,
> 			     );
> my @seq = $dbc->get_all_primary_ids;
> print "got @seq\n";
> 
> my $thing = $dbc->get_Seq_by_acc($seq[0]);
> print "got $thing\n";
> 
> my @a = $thing->top_SeqFeatures;
> 
> my $ad = $dbc->_adaptor;
> print $ad->list_bioentry_ids('test'),"\n";
> 
> -- 
> ==============================================================
> ==========
> Lincoln D. Stein                           Cold Spring Harbor 
> Laboratory
> lstein@cshl.org			                  Cold 
> Spring Harbor, NY
> Positions available at my lab: see http://stein.cshl.org/#hire
> ==============================================================
> ==========
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