[BioSQL-l] BioSQL Schema problem

[Hilmar Lapp]

The biosqldb-views-pg.sql is badly outdated I notice. Sorry about  
that. Are you sure you need it? (Most applications will not.)

I probably shouldn't just delete but try to update it. The offending  
seqfeature_key table has long been removed from the schema and you  
can safely delete the view definition from the file, but there may be  
a few more errors given its age.

I need to investigate the script's failure on inserting nodes - this  
is assuming that you put the file by hand in the right place.  
Apparently there is an alphanumerical value that gets parsed as the  
taxon id (which must be numeric indeed).

--download is a switch and hence does not take any arguments, -- 
download 0 does ask to download, which is why you see the error. I  
don't know why the download fails, maybe there's a problem with  
extended ftp mode (EPSV/EPRT commands) but I don't know off hand how  
you disable them in Net::FTP.

	-hilmar

On Jun 28, 2006, at 8:28 AM, Samuel Thoraval wrote:

>
> Hello,
>
> I am new to biosql and I have 2 problems installing last CVS version
> (*1.4.2.1*, /Sun Jun 16)/:
> - running biosqldb-views-pg.sql after biosqldb-pg.sql gives errors,  
> the
> first one being:
> psql:biosqldb-views-pg.sql:6: ERROR:  relation "seqfeature_key"  
> does not
> exist
> - running load_ncbi_taxonomy.pl with
> ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
> <ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz> (the script
> download option set to 1 doesn't download anything) gives the  
> following
> error :
> ---------------------------------------------------------------------- 
> ------------------------------------------------------------------
>  ./scripts/load_ncbi_taxonomy.pl --dbname bioseqdb --driver Pg -- 
> download 0
> gunzip: taxdata/taxdump.tar.gz: No such file or directory
> tar: taxdump.tar: ne peut open: Aucun fichier ou répertoire de ce type
> tar: Erreur non récupérable: fin de l'exécution immédiate
> Loading NCBI taxon database in taxdata:
>         ... retrieving all taxon nodes in the database
>         ... reading in taxon nodes from nodes.dmp
>         ... insert / update / delete taxon nodes
> failed to insert node (1;1;1;no rank;1;0): ERROR:  column  
> "taxon_id" is
> of type integer but expression is of type character varying
> HINT:  You will need to rewrite or cast the expression.
> ---------------------------------------------------------------------- 
> ------------------------------------------------------------------
>
> The schema expected from the biosqldb-views-pg.sql or taxonomy dump
> file  does not match  the one in biosqldb-pg.sql.
>
>
> Best regards,
>
> -- 
> Samuel Thoraval
> LIBROPHYT, Bioinformatique
> Centre de Cadarache
> Bâtiment 185, DEVM
> 13108 St Paul-Lez-Durance
> France
> Tél:  +33 442 574 799
> Fax: +33 442 574 439
> e-mail : samuel.thoraval at librophyt.com
>
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>

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