[Bioperl-l] bioperl-db question

Hilmar Lapp hlapp at gmx.net
Mon Nov 20 16:28:29 EST 2006


It looks like you are using the MySQL schema under Oracle. There are  
different DDL scripts for each supported RDBMS. The ones for Oracle  
are in the sql/biosql-ora subdirectory. Note the INSTALL document in  
that directory.

	-hilmar


On Nov 20, 2006, at 1:16 PM, gang wu wrote:

> Hi Hilmar,
>
> Below is the output. Thanks.
>
> Gang
> ==========================================================
> [root at elegans bioperl-db-1.5.2-RC3]# export HARNESS_VERBOSE=1
> [root at elegans bioperl-db-1.5.2-RC3]# make test_01dbadaptor  
> TEST_VERBOSE=1
> PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib -I/usr/lib64/ 
> perl5/5.8.5/x86_64-linux-thread-multi -I/usr/lib/perl5/5.8.5 -e  
> 'use Test::Harness qw(&runtests $verbose); $verbose=1; runtests  
> @ARGV;' t/01dbadaptor.t
> t/01dbadaptor....1..19
> ok 1
> ok 2
> ok 3
> ok 4
> ok 5
> ok 6
> ok 7
> ok 8
> ok 9
> ok 10
> ok 11
> attempting to load adaptor class for BioNamespace
> ok 12
>        attempting to load module Bio::DB::BioSQL::BioNamespaceAdaptor
> instantiating adaptor class Bio::DB::BioSQL::BioNamespaceAdaptor
> ok 13
> ok 14
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::BioNamespaceAdaptor
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::BasePersistenceAdaptor
> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as  
> driver peer for Bio::DB::BioSQL::BioNamespaceAdaptor
> preparing UK select statement: SELECT biodatabase.oid,  
> biodatabase.name, biodatabase.authority FROM biodatabase WHERE name  
> = ?
> DBD::Oracle::db prepare failed: ORA-00904: "BIODATABASE"."OID":  
> invalid identifier (DBD ERROR: error possibly near <*> indicator at  
> char 7 in 'SELECT <*>biodatabase.oid, biodatabase.name,  
> biodatabase.authority FROM biodatabase WHERE name = :p1') [for  
> Statement "SELECT biodatabase.oid, biodatabase.name,  
> biodatabase.authority FROM biodatabase WHERE name = ?"] at blib/lib/ 
> Bio/DB/BioSQL/BaseDriver.pm line 1800.
> BioNamespaceAdaptor: binding UK column 1 to "__dummy__" (namespace)
> Can't call method "bind_param" on an undefined value at blib/lib/ 
> Bio/DB/BioSQL/BasePersistenceAdaptor.pm line 939.
> dubious
>        Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 15-19
>        Failed 5/19 tests, 73.68% okay
> Failed Test     Stat Wstat Total Fail  Failed  List of Failed
> ---------------------------------------------------------------------- 
> ---------
> t/01dbadaptor.t  255 65280    19   10  52.63%  15-19
> Failed 1/1 test scripts, 0.00% okay. 5/19 subtests failed, 73.68%  
> okay.
> make: *** [test_01dbadaptor] Error 2
> =========================================================
>
>
> Hilmar Lapp wrote:
>> Hi Gang,
>>
>> what I wanted to get at was the error message from the driver when  
>> it fails to generate the prepared statement, but this is not in  
>> the output.
>>
>> I believe you need set the HARNESS_VERBOSE environment variable to  
>> 1 before testing to get what I need:
>>
>>     $ export HARNESS_VERBOSE=1 # or setenv HARNESS_VERBOSE 1 for  
>> csh/tcsh
>>     $ make test_01dbadaptor TEST_VERBOSE=1
>>
>> This will lead to _a lot_ of debugging output. Do not run this for  
>> the entire test suite.
>>
>> The errors for mysql I believe are related to the fact that have  
>> loaded the NCBI taxonomy before testing? Run the tests on a fresh  
>> (completely empty) instance of BioSQL.
>>
>> Let me know what you get for the Oracle test above.
>>
>>     -hilmar
>>
>> On Nov 20, 2006, at 10:57 AM, gang wu 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
>>
>> --===========================================================
>> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
>> ===========================================================
>>
>>
>>
>>
>>

-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
===========================================================







More information about the Bioperl-l mailing list