[Bioperl-l] bioperl-db question

Chris Fields 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
driver/configuration.

> > 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!  

Chris



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