[Bioperl-l] bioperl-db question

gang wu 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
> 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.
>   

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!  
>
> Chris
>
>   



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