[Bioperl-l] bioperl-db question
gwu at molbio.mgh.harvard.edu
Mon Nov 20 15:34:07 EST 2006
Chris Fields wrote:
>> 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.
Can not change 'Oracle' to 'oracle', the DBD driver name is DBD::Oracle.
It's an odd naming inconsistence. MySQL DBD driver name is DBD::mysql.
How about PostgreSQL DBD driver naming?
> Hopefully that isn't your real password!
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