[BioSQL-l] GBrowse on BioSQL dead in water again
Hilmar Lapp
hlapp@gnf.org
Wed, 9 Oct 2002 01:42:38 -0700
The new adaptors work in a completely different way, and you're
generally not supposed to instantiate them directly. It's like the
SeqIO system in this regard.
I don't know exactly what the problem is with cascades of objects,
but I'm not worried that I wouldn't be able to re-implement the
functionality that is needed to support Das. I was just saying that
if anyone is willing to help he/she is greatly welcome.
Don't forget that the branch code is (should be) in perfect working
order, so I'm not exactly sure what the problem is right now. Das is
still working off of biosql and Gbrowse should still be running
nicely off of Biosql if you use the branch.
The HEAD is not stable yet, you shouldn't use it anyway unless you
want to help developing it.
-hilmar
On Wednesday, October 9, 2002, at 12:51 AM, Elia Stupka wrote:
> 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
>>> ==============================================================
>>> ==========
>>> _______________________________________________
>>> BioSQL-l mailing list
>>> BioSQL-l@open-bio.org
>>> http://open-bio.org/mailman/listinfo/biosql-l
>>>
>>
>
>
--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
-------------------------------------------------------------