[Biopython-dev] [Bug 2395] Need a commit in BioSQL with MySQL

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2395





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2007-11-14 04:17 EST -------
In an email Eric Gibert wrote:
> MySQL does not commit the transaction by default and autocommit
> is not so advisable to ensure the database integrity. Thus we
> could include a <database>.adaptor.commit() at the end of the
> following functions:
>
> Loader.py: load_seqrecord and remove
> BioSeqDatabase: DBServer.remove_database, new_database, load_database_sql
> BioSeqDatabase.Load (which might be redundant with commit in Loader)

I had also been wondering about something like this.

However, We need to think about the other database engines not just MySQL.  And
we need to think about how this would affect anyone trying to use SQL
transactions.

Also, doing a commit in Loader.py's load() method after all the records, might
be better than in load_seqrecord() after each record.  That way we should load
either all the records or none.  Otherwise if the process fails half way, we
would have only half the records commited and that would be more difficult for
the user to sort out.


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