[BioSQL-l] PostgreSQL Error: column "oid" does not exist

[Hilmar Lapp]

I think this can be considered a bug in the Pg version of BioSQL and  
needs to be fixed.

It is also a nice example for how things come back to you and bite.  
At the time I wrote the RULEs (the OID doesn't appear anywhere else  
does it?) PostgreSQL didn't have nested transactions and so the RULE  
statements really were a kludge to the absence of nested transaction,  
which is what I would have really wanted.

I think it is time now to get rid of that stuff by implementing the  
respective parts in bioperl-db using nested transactions, thereby  
obviating the need for RULE statements, thereby obviating the need  
for putting 'WITH OID' anywhere.

	-hilmar

On Aug 7, 2006, at 2:32 PM, Roy Chaudhuri wrote:

> Hi all.
>
> I've just been playing around with a new install of PostgreSQL  
> v8.14. I
> was getting lots of error messages saying 'column "oid" does not  
> exist'
> when I loaded the BioSQL schema (biosqldb-pg.sql). After a bit of
> research I found out that the default value for default_with_oids has
> changed from true to false for PostgreSQL 8.1 onwards:
> http://www.postgresql.org/docs/8.1/static/runtime-config- 
> compatible.html#GUC-DEFAULT-WITH-OIDS
>
> Altering the BioSQL table definitions to explicitly state 'WITH OIDS'
> before the semicolon works as a fix. Perhaps this could be changed in
> the CVS?
>
> Sorry if this seems obvious to Pg experts but it would have saved a
> novice like me a bit of time had I found mention of it in the mailing
> list archives.
>
> Cheers,
> Roy.
>
> --
> Dr. Roy Chaudhuri
> Bioinformatics Research Fellow
> Division of Immunity and Infection
> University of Birmingham, U.K.
>
> http://xbase.bham.ac.uk
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l
>

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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