[BioSQL-l] GBrowse on BioSQL dead in water again

[Elia Stupka]

Hi Hilmar and Lincoln,

Hilmar note that the problem is precisely the fact that Lincoln relied on a
branch module, which BioDatabaseAdaptor. This module was the most
straightforward way to call one new method (not a cascade of objects and
methods) to do both a)connection to a biosql database and b)getting the
adaptor for one particular biological database.

Das was already working off biosql thanks to the work that Lincoln did and
GBrowse was already running nicely on the DasI interface to a single
biological database within biosql.

So all is needed is *not to remove* that object, and all would be back to
normal.

Elia


----- Original Message -----
From: "Hilmar Lapp" <hlapp@gnf.org>
To: <lstein@cshl.org>; "elia@gugu-sg.org" <elia@fugu-sg.org>
Cc: <bioperl-l@bio.perl.org>; <biosql-l@open-bio.org>
Sent: Wednesday, October 09, 2002 5:29 AM
Subject: RE: [BioSQL-l] GBrowse on BioSQL dead in water again


> 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
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
>
> > -----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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> > BioSQL-l@open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l
> >
>