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

[Lincoln Stein]

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