[Open-bio-l] BioSQL Schema problem
Samuel Thoraval
samuel.thoraval at librophyt.com
Wed Jun 28 09:45:00 UTC 2006
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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