[Bioperl-l] bioperl-db question
cjfields at uiuc.edu
Mon Nov 20 15:19:56 EST 2006
> You are right, all tests can pass for MySQL after unloading
> NCBI Taxonomy data. But output for Oracle tests were not
> affected. Thanks.
Yes, the oracle tests were by far the worst, which suggests something in the
> > As for the rest, could it be the DBharness.biosql.conf file setup,
> > which assumes MySQL by default? If you switch to Oracle
> you have to
> > indicate the proper DBD driver in the conf file:
> > ...
> > # DBD driver to use - mandatory
> > 'driver' => 'oracle',
> > ...
> I did change the configuration, or it can not pass the DBI
> connection tests. Below is part of my parameters:
> 'driver' => 'Oracle',
> 'host' => 'elegans',
> 'user' => 'biosqldb_sgowner',
> 'port' => '1521',
> 'password' => 'pass',
> 'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'],
> 'dbname' => 'oracle_sid',
> 'database' => 'biosql',
Try changing the driver to all lower case (i.e. from 'Oracle' to 'oracle').
Also, the schema_sql is still set to the mysql schema (not oracle). That
shouldn't make a difference, but you never know.
Hopefully that isn't your real password!
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