[Bioperl-l] postgres 8.3 - load_seqdatabase.pl / swissprot

[Erik]

On Sat, March 22, 2008 20:30, Hilmar Lapp wrote:

> SELECT * FROM taxon WHERE ncbi_taxon_id = 326939;

No, I don't seem to have that particular id, although I
ran the ncbi load script yesterday just before the sprot. 
Btw, in the meantime I figured out that it was a parsing
error choking on an unexpected period.

You asked for preceding errors, but there were none.

I have now restarted the same uniprot_sprot.dat load with
--safe, which if I understand you correctly will just skip
any non-parsable records.


And wrt the postgres 8.3 casting:

I only added the first cast of the list of Peter Eisentraut:

CREATE FUNCTION pg_catalog.text(integer) RETURNS text
STRICT IMMUTABLE LANGUAGE SQL AS 'SELECT
textin(int4out($1));'; --added 20080322
CREATE CAST (integer AS text) WITH FUNCTION
pg_catalog.text(integer) AS IMPLICIT; --added 20080322

I hope eventually a more durable solution will be found -
I fear this reinstalling of old casting functionality will
generate unexpected problems of it's own.

But it seems a good intermediary solution; with it, the
previously failing t/16odba.t succeeds...


Thank you,

Erik Rijkers