[Bioperl-l] bioperl-db question

gang wu gwu at molbio.mgh.harvard.edu
Tue Nov 21 03:11:03 EST 2006


Can you show me where it indicates I am actually using the MySQL schema. 
I am pretty sure that I used the sql script files from 
sql/biosql-ora(Has anyone actually tried to install MySQL schema on 
Oracle?). I can reinstall the schema if you think that's the way to 
solve the problem.  Thanks very much.

Gang

Hilmar Lapp wrote:
> 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 :
>>> ===========================================================
>>>
>>>
>>>
>>>
>>>
>>>       
>
>   



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