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

[Hilmar Lapp]

Will do. Hopefully it's not too long until then ... (my estimate is 
it is a matter of weeks)

	-hilmar

On Thursday, October 10, 2002, at 08:14 AM, Lincoln Stein wrote:

> I'm sorry I missed the announcements.  I will put a note about 
> using the right
> branch in the DAS and GBrowse documentation.  DAS support is very 
> easy to do
> since it runs on top of the Bio::SeqI and Bio::SeqFeatureI API.  
> When the
> adaptors are stable, just explain to me how to use them and I'll 
> make the
> appropriate changes.
>
> Lincoln
>
> On Tuesday 08 October 2002 10:01 pm, Hilmar Lapp wrote:
>> 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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