[Bioperl-l] Error in loading into biosql database

[Hilmar Lapp]

I guess you need to re-initialize (truncate) your species database.  
There may have been left-overs.

The situation that leads to the stack trace and exception below occurs  
in one specific situation, namely if the species at hand already exists  
in the database (from a previous insert), but without the NCBI taxonID.  
If the same species passes through again, but this time with an NCBI  
taxonID set, it is looked up by the NCBI taxonID. This look-up fails.  
Then the adaptor tries to insert the species, which also fails, because  
the species is actually already there, just incomplete.

This should not happen if you start from swissprot, as swissprot  
supposedly always gives you the taxon ID.

If you never inserted Homo sapiens by hand, and could not possibly have  
loaded it from a datafile that lacked NCBI taxon IDs (I believe that  
e.g. the embl parser doesn't catch the ID in the feature table), then  
it is possibly a left-over from running the tests, which means you run  
MySQL without transactions enabled. I'd fix that first if it is true.

	-hilmar

On Wednesday, March 19, 2003, at 01:04  PM, Siddhartha Basu wrote:

> Hi,
> It was a multiple version problem. So i loaded everything freshly and  
> the earlier errors have disappeared. But now it seems to be failing  
> with different errors....
>
> ======================================================================= 
> =
> DBD::mysql::st execute failed: Duplicate entry 'Homo sapiens--' for  
> key 3 at /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm  
> line 564, <GEN0> line 310.
>
> -------------------- WARNING ---------------------
> MSG: insert in Bio::DB::BioSQL::SpeciesAdaptor (driver) failed, values  
> were  
> ("Human","sapiens:Homo:Hominidae:Catarrhini:Primates:Eutheria:Mammalia: 
> Euteleostomi:Vertebrata:Craniata:Chordata:Metazoa:Eukaryota","9606","Ho 
> mo sapiens","-") FKs ()
> Duplicate entry 'Homo sapiens--' for key 3
> ---------------------------------------------------
>
> ------------- EXCEPTION  -------------
> MSG: Could not store P42655:
> ------------- EXCEPTION  -------------
> MSG: create: object (Bio::Species) failed to insert or to be found by  
> unique key
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:197
> STACK Bio::DB::Persistent::PersistentObject::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:242
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:169
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:240
> STACK Bio::DB::Persistent::PersistentObject::store  
> /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/ 
> PersistentObject.pm:266
> STACK (eval) load_seqdatabase.pl:424
> STACK toplevel load_seqdatabase.pl:423
>
> --------------------------------------
>
>
> STACK toplevel load_seqdatabase.pl:433
>
> --------------------------------------
>
> ======================================================================= 
> ===
>
> This is the error i am getting while i tried to load the swissprot  
> format of whole human proteome released by ebi. I am also getting  
> similar kind of multiple errors even if i use the file for mouse  
> proteome and the locuslink LL_tmpl file.
>
> Any idea what's happening now.
>
> siddhartha
>
>
> Hilmar Lapp wrote:
>
>> This means you're not running the before-singapore-change branch of   
>> bioperl-db. The offending table only came in after that tag. Maybe a   
>> multiple version / forgotten purge problem?
>>     -hilmar
>
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------