[Bioperl-l] bioperl-db question

gang wu gwu at molbio.mgh.harvard.edu
Mon Nov 20 14:40:56 EST 2006


Chris Fields wrote:
>> Hi Hilmar,
>>
>> Thanks for your message. Below are several tests for Oracle 
>> and MySQL. 
>> MySQL actually also has two tests with failed items which may 
>> be related to data in BioSQL database.
>>
>> Could it be my Oracle installation/configuration has some issues?
>>
>> Thanks.
>>
>> Gang
>>     
>
> ...
>
> You stated in a previous post that you had preloaded taxonomy; the various
> species test fails may be from that.  Hilmar pointed out in a previous
> thread that tests require a BioSQL database without NCBI taxonomy loaded
> (i.e. just the schema).  The INSTALL doc should now state that.
>   
You are right, all tests can pass for MySQL after unloading NCBI 
Taxonomy data. But output for Oracle tests were not affected. Thanks.
> 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',

> Chris
>
>
>   
>> Hilmar Lapp wrote:
>>     
>>> This is very odd. I would mean that preparing the statement failed, 
>>> i.e., that the generated SQL was not accepted by the server (or the 
>>> Oracle client library).
>>>
>>> Which test does this happen with?
>>>
>>> Could you run the test alone in which it happens with TEST_VERBOSE 
>>> turned on? E.g.,
>>>
>>>     $ make test_03simpleseq TEST_VERBOSE=1
>>>
>>> if it's the simpleseq test that's causing the failure. Capture the 
>>> output in a file and send it to me.
>>>
>>>     -hilmar
>>>
>>> On Nov 18, 2006, at 3:57 AM, gang wu wrote:
>>>
>>>       
>>>> Hi everyone,
>>>>
>>>> I used to use MySQL to host the BioSQL schema and load 
>>>>         
>> Genbank into it
>>     
>>>> with the 'load_seqdatabase.pl' without problem(except 
>>>>         
>> extremely slow. It
>>     
>>>> took about 12 hours to load Arabidopsis thaliana). I just 
>>>>         
>> loaded the
>>     
>>>> BioSQL schema in Oracle 10g. I could load NCBI Taxonomy 
>>>>         
>> database without
>>     
>>>> problem.
>>>>
>>>> When I 'make test' with bioperl-db-1.5.2.R3, all tests can 
>>>>         
>> pass with
>>     
>>>> MySQL while always saw an error with Oracle:
>>>>       Can't call method "bind_param" on an undefined value at
>>>>
>>>>         
>> /root/.cpan/build/bioperl-db-1.5.2-RC3/blib/lib/Bio/DB/BioSQL/
>>     
> BasePersistenceAdaptor.pm 
>   
>>>> line 939.
>>>>
>>>> , where the code is $sth->bind_param();
>>>>
>>>> Any idea what the problem is?
>>>>
>>>> Gang
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>         
>>> --===========================================================
>>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>>       
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>     
>
>   



More information about the Bioperl-l mailing list