[Biopython-dev] [Bug 2833] Features insertion on previous bioentry_id

Hilmar Lapp hlapp at gmx.net
Fri May 22 02:05:17 UTC 2009

On May 21, 2009, at 6:52 PM, Cymon Cox wrote:

> [...]
> Hi Andrea,
> The problem appears to be related to the BioSQL schema/PostGreSQL.
> As you indicated, adding a duplicate entry to bioentry returns a  
> 0" and doesnt throw an IntegrityError which is what the code is  
> looking from
> and presumably what MySQL throws.
> The reason it doesnt throw an error is because of one (or both) of  
> the RULES
> in the schema:

Indeed, I'd almost forgotten. The rules are there mostly as a remnant  
from earlier versions of PostgreSQL to support transactional loading  
the way bioperl-db (the object-relational mapping for BioPerl) is  
optimized. You probably don't need them anywhere else.


Bioperl-db is optimized such that entities that very likely don't  
exist yet in the database are attempted for insert right away. If the  
insert fails due to a unique key violation, the record is looked up  
(and then expected to be found). In Oracle and MySQL you can do this  
and the transaction remains healthy; i.e., you can commit the  
transaction later and all statements except those that failed will be  
committed. In PostgreSQL any failed statement dooms the entire  
transaction, and the only way out is a rollback. In this case, if you  
want the loading of one sequence record as one transaction, failing to  
insert a single feature record will doom the entire sequence load and  
you would need to start over with the sequence. To fix this, I wrote  
the rules, which in essence do do the lookups for PostgreSQL that the  
bioperl-db code would otherwise avoid, and on insert do nothing if the  
record is found, which results in zero rows affected when you would  
expect one (which is what bioperl-db cues off of and then triggers a  
The right way to do this meanwhile is to use nested transactions,  
which PostgreSQL supports since v8.0.x, but I haven't gotten around to  
implement support for that in Bioperl-db.

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

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